10mh
|
transferase-DNA |
X-ray (2.55 Å) |
Sheikhnejad G, Brank A, Christman JK, Goddard A,
Alvarez E, Ford Jr H, Marquez VE, Marasco CJ, Sufrin JR,
O'gara M, Cheng X |
(1999) "Mechanism
of inhibition of DNA (cytosine C5)-methyltransferases
by oligodeoxyribonucleotides containing
5,6-dihydro-5-azacytosine." J.Mol.Biol.,
285, 2021-2034. doi: 10.1006/jmbi.1998.2426.
|
Ternary structure of hhai methyltransferase with adohcy
and hemimethylated DNA containing
5,6-dihydro-5-azacytosine at the target . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
1bsu
|
hydrolase-DNA |
X-ray (2.0 Å) |
Martin AM, Sam MD, Reich NO, Perona JJ |
(1999) "Structural
and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease." Nat.Struct.Biol.,
6, 269-277. doi: 10.1038/6707.
|
Structural and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease . ➥(2) [+]:Acg/cgT, [-]:cgT/Acg,
is-WC-paired, is-in-duplex, other-contacts
|
1dct
|
transferase-DNA |
X-ray (2.8 Å) |
Reinisch KM, Chen L, Verdine GL, Lipscomb WN |
(1995) "The
crystal structure of HaeIII methyltransferase
convalently complexed to DNA: an extrahelical cytosine
and rearranged base pairing."
Cell(Cambridge,Mass.), 82,
143-153. doi: 10.1016/0092-8674(95)90060-8.
|
DNA (cytosine-5) methylase from haeiii covalently bound
to DNA . ➥(2) [-]:GGC/GcC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
stacking-with-AA
|
1ig4
|
transcription-DNA |
NMR |
Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T,
Nakao M, Shirakawa M |
(2001) "Solution
structure of the methyl-CpG binding domain of human
MBD1 in complex with methylated DNA."
Cell(Cambridge,Mass.), 105,
487-497. doi: 10.1016/S0092-8674(01)00324-5.
|
Solution structure of the methyl-cpg-binding domain of
human mbd1 in complex with methylated DNA .
➥(2) [+]:CcG/cGG, [-]:cGG/CcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
other-contacts
|
2c7o
|
transferase-DNA |
X-ray (1.9 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with 13mer
oligonucleotide containing 2-aminopurine adjacent to
the target base (pcgc:gmgc) and sah . ➥(1) [+]:GcC/gGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2c7p
|
transferase-DNA |
X-ray (1.7 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with oligonucleotide
containing 2- aminopurine opposite to the target base
(gcgc:gmpc) and sah . ➥(1)
[+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2c7q
|
transferase-DNA |
X-ray (1.85 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with oligonucleotide
containing 2- aminopurine outside the recognition
sequence (paired with g) and sah . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2c7r
|
transferase-DNA |
X-ray (1.9 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase (t250g mutant) complex with
oligonucleotide containing 2-aminopurine as a target
base (gpgc:gmgc) and sah . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2ky8
|
transcription-DNA |
NMR |
Scarsdale JN, Webb HD, Ginder GD, Williams DC |
(2011) "Solution
structure and dynamic analysis of chicken MBD2 methyl
binding domain bound to a target-methylated DNA
sequence." Nucleic Acids Res.,
39, 6741-6752. doi: 10.1093/nar/gkr262.
|
Solution structure and dynamic analysis of chicken mbd2
methyl binding domain bound to a target methylated DNA
sequence . ➥(2) [+]:TcG/cGA, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
2moe
|
hydrolase-DNA |
NMR |
Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN,
Williams DC |
(2015) "Solution
structure and intramolecular exchange of
methyl-cytosine binding domain protein 4 (MBD4) on DNA
suggests a mechanism to scan for mCpG/TpG
mismatches." Nucleic Acids Res.,
42, 11218-11232. doi: 10.1093/nar/gku782.
|
Solution structure of mbd4 methyl-cytosine binding
domain bound to methylated DNA . ➥(1) [-]:cGG/CcG, is-WC-paired,
is-in-duplex, other-contacts
|
2uyc
|
transferase |
X-ray (2.0 Å) |
Daujotyte D, Grazulis S |
"HhaI DNA Methyltransferase R163N Mutant Complex with
13mer Gcgc-Gmgc Oligonucleotide and Sah." |
Hhai DNA methyltransferase r163n mutant complex with
13mer gcgc-gmgc oligonucleotide and sah . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2uyh
|
transferase |
X-ray (2.63 Å) |
Daujotyte D, Grazulis S |
"HhaI DNA Methyltransferase S87Q-Q237S Mutant Complex
with 13mer Gcgc-Gmgc Oligonucleotide and Sah." |
Hhai DNA methyltransferase s87q-q237s mutant complex
with 13mer gcgc- gmgc oligonucleotide and sah .
➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2uz4
|
transferase |
X-ray (2.1 Å) |
Daujotyte D, Leinartaite L, Grazulis S |
"DNA Methyltransferase R165N Mutant." |
Hhai DNA methyltransferase r165n mutant complex with
13mer gcgc-gmgc oligonucleotide and sah . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
2zkd
|
ligase |
X-ray (1.6 Å) |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa
M |
(2008) "Recognition
of hemi-methylated DNA by the SRA protein UHRF1 by a
base-flipping mechanism." Nature,
455, 818-821. doi: 10.1038/nature07249.
|
Crystal structure of the sra domain of mouse np95 in
complex with hemi-methylated cpg DNA . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
2zke
|
ligase |
X-ray (2.6 Å) |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa
M |
(2008) "Recognition
of hemi-methylated DNA by the SRA protein UHRF1 by a
base-flipping mechanism." Nature,
455, 818-821. doi: 10.1038/nature07249.
|
Crystal structure of the sra domain of mouse np95 in
complex with hemi-methylated cpg DNA . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
2zkf
|
ligase |
X-ray (2.55 Å) |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa
M |
(2008) "Recognition
of hemi-methylated DNA by the SRA protein UHRF1 by a
base-flipping mechanism." Nature,
455, 818-821. doi: 10.1038/nature07249.
|
Crystal structure of the sra domain of mouse np95 in
complex with hemi-methylated cpg DNA . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
2zo0
|
ligase-DNA |
X-ray (2.19 Å) |
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen
SE, Cheng X |
(2008) "The SRA
domain of UHRF1 flips 5-methylcytosine out of the DNA
helix." Nature, 455,
826-829. doi: 10.1038/nature07280.
|
Mouse np95 sra domain DNA specific complex 1 .
➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
2zo1
|
ligase-DNA |
X-ray (1.96 Å) |
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen
SE, Cheng X |
(2008) "The SRA
domain of UHRF1 flips 5-methylcytosine out of the DNA
helix." Nature, 455,
826-829. doi: 10.1038/nature07280.
|
Mouse np95 sra domain DNA specific complex 2 .
➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3c2i
|
transcription regulator |
X-ray (2.5 Å) |
Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP,
Walkinshaw MD |
(2008) "MeCP2
binding to DNA depends upon hydration at
methyl-CpG." Mol.Cell,
29, 525-531. doi: 10.1016/j.molcel.2007.12.028.
|
The crystal structure of methyl-cpg binding domain of
human mecp2 in complex with a methylated DNA sequence
from bdnf . ➥(2) [+]:AcG/cGT, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
3clz
|
ligase |
X-ray (2.2 Å) |
Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner
C, Arrowsmith CH, Dhe-Paganon S |
(2008) "Structural
basis for recognition of hemi-methylated DNA by the SRA
domain of human UHRF1." Nature,
455, 822-825. doi: 10.1038/nature07273.
|
The set and ring associated (sra) domain of uhrf1 bound
to methylated DNA . ➥(4)
not-WC-paired,
not-in-duplex, stacking-with-AA
|
3f8i
|
ligase-DNA |
X-ray (2.29 Å) |
Hashimoto H, Horton JR, Zhang X, Cheng X |
(2009) "UHRF1, a
modular multi-domain protein, regulates
replication-coupled crosstalk between DNA methylation
and histone modifications." Epigenetics,
4, 8-14.
|
Mouse uhrf1 sra domain bound with hemi-methylated cpg,
crystal structure in space group p21 . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3f8j
|
ligase-DNA |
X-ray (1.99 Å) |
Hashimoto H, Horton JR, Zhang X, Cheng X |
(2009) "UHRF1, a
modular multi-domain protein, regulates
replication-coupled crosstalk between DNA methylation
and histone modifications." Epigenetics,
4, 8-14.
|
Mouse uhrf1 sra domain bound with hemi-methylated cpg,
crystal structure in space group c222(1) . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3fde
|
ligase |
X-ray (1.41 Å) |
Hashimoto H, Horton JR, Zhang X, Cheng X |
(2009) "UHRF1, a
modular multi-domain protein, regulates
replication-coupled crosstalk between DNA methylation
and histone modifications." Epigenetics,
4, 8-14.
|
Mouse uhrf1 sra domain bound with hemi-methylated cpg
DNA, crystal structure in space group c222(1) at 1.4 Å
resolution . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3q0b
|
transferase-DNA |
X-ray (2.2 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra- fully methylated cg DNA
complex in space group p42212 . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3q0c
|
transferase-DNA |
X-ray (2.66 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra-fully methylated cg DNA
complex in space group p6122 . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3q0d
|
transferase-DNA |
X-ray (2.37 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra- hemi methylated cg DNA
complex . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3q0f
|
transferase-DNA |
X-ray (2.75 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra- methylated chh DNA
complex . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3ssc
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Sukackaite R, Grazulis S, Tamulaitis G, Siksnys
V |
(2012) "The
recognition domain of the methyl-specific endonuclease
McrBC flips out 5-methylcytosine." Nucleic
Acids Res., 40, 7552-7562. doi:
10.1093/nar/gks332.
|
DNA binding domain of restriction endonuclease bound to
DNA . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3ssd
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Sukackaite R, Grazulis S, Tamulaitis G, Siksnys
V |
(2012) "The
recognition domain of the methyl-specific endonuclease
McrBC flips out 5-methylcytosine." Nucleic
Acids Res., 40, 7552-7562. doi:
10.1093/nar/gks332.
|
DNA binding domain of restriction endonuclease bound to
DNA . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
3vxv
|
hydrolase-DNA |
X-ray (2.0 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of methyl cpg binding domain of mbd4
in complex with the 5mcg-tg sequence . ➥(1) [+]:CcG/TGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
3vxx
|
hydrolase-DNA |
X-ray (2.204 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of methyl cpg binding domain of mbd4
in complex with the 5mcg-5mcg sequence . ➥(2) [+]:CcG/cGG, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
3vyb
|
hydrolase-DNA |
X-ray (2.4 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of methyl cpg binding domain of mbd4
in complex with the 5mcg-hmcg sequence . ➥(1) [+]:CcG/cGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
3vyq
|
hydrolase-DNA |
X-ray (2.525 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of the methyl cpg binding domain of
mbd4 in complex with the 5mcg-tg sequence in space
group p1 . ➥(1) [+]:CcG/TGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
4aqu
|
hydrolase |
X-ray (2.3 Å) |
Valton J, Daboussi F, Leduc S, Molina R, Redondo P,
Macmaster R, Montoya G, Duchateau P |
(2012) "5'-Cytosine-Phosphoguanine
(Cpg) Methylation Impacts the Activity of Natural and
Engineered Meganucleases." J.Biol.Chem.,
287, 30139. doi: 10.1074/JBC.M112.379966.
|
Crystal structure of i-crei complexed with its target
methylated at position plus 2 (in the b strand) in the
presence of calcium . ➥(1)
[-]:CGT/AcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
4aqx
|
hydrolase |
X-ray (2.2 Å) |
Valton J, Daboussi F, Leduc S, Molina R, Redondo P,
Macmaster R, Montoya G, Duchateau P |
(2012) "5'-Cytosine-Phosphoguanine
(Cpg) Methylation Impacts the Activity of Natural and
Engineered Meganucleases." J.Biol.Chem.,
287, 30139. doi: 10.1074/JBC.M112.379966.
|
Crystal structure of i-crei complexed with its target
methylated at position plus 2 (in the b strand) in the
presence of magnesium . ➥(1)
[-]:CGT/AcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
4da4
|
transferase-DNA |
X-ray (2.6 Å) |
Song J, Teplova M, Ishibe-Murakami S, Patel DJ |
(2012) "Structure-Based
Mechanistic Insights into DNMT1-Mediated Maintenance
DNA Methylation." Science,
335, 709-712. doi: 10.1126/science.1214453.
|
Structure of mouse dnmt1 (731-1602) bound to
hemimethylated cpg DNA . ➥(2)
[+]:CcG/GGG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
4dkj
|
transferase-DNA |
X-ray (2.15 Å) |
Wojciechowski M, Czapinska H, Bochtler M |
(2013) "CpG
underrepresentation and the bacterial CpG-specific DNA
methyltransferase M.MpeI."
Proc.Natl.Acad.Sci.USA, 110,
105-110. doi: 10.1073/pnas.1207986110.
|
Cpg specific methyltransferase in complex with target
DNA . ➥(1) [-]:GGC/GcC, is-WC-paired,
is-in-duplex, stacking-with-AA
|
4f6n
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Buck-Koehntop BA, Stanfield RL, Ekiert DC,
Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE |
(2012) "Molecular
basis for recognition of methylated and specific DNA
sequences by the zinc finger protein Kaiso."
Proc.Natl.Acad.Sci.USA, 109,
15229-15234. doi: 10.1073/pnas.1213726109.
|
Crystal structure of kaiso zinc finger DNA binding
protein in complex with methylated cpg site DNA .
➥(4) [+]:CcG/cGG, [+]:GcG/cGc,
[-]:cGT/AcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
4gjp
|
transcription-DNA |
X-ray (1.94 Å) |
Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG |
"Crystal structure of a protein complex." |
Crystal structure of the tal effector dhax3 bound to
dsDNA containing repetitive methyl-cpg . ➥(4) [+]:GcG/CGC, [+]:TcG/CGA,
is-WC-paired, is-in-duplex, stacking-with-AA
|
4gjr
|
transcription-DNA |
X-ray (1.85 Å) |
Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG |
"Crystal structure of a protein complex." |
Crystal structure of the tal effector dhax3 bound to
methylated dsDNA . ➥(6)
[+]:AcC/GGT,
[+]:CcC/GGG, [+]:TcT/AGA, hydrophobic-with-AA,
is-WC-paired, is-in-duplex, stacking-with-AA
|
4gzn
|
transcription-DNA |
X-ray (0.99 Å) |
Liu Y, Toh H, Sasaki H, Zhang X, Cheng X |
(2012) "An
atomic model of Zfp57 recognition of CpG methylation
within a specific DNA sequence." Genes
Dev., 26, 2374-2379. doi:
10.1101/gad.202200.112.
|
Mouse zfp57 zinc fingers in complex with methylated DNA
. ➥(2) [+]:CcG/cGG, [-]:cGC/GcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
4hp1
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y,
Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q,
Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB,
Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG |
(2012) "Tet3
CXXC Domain and Dioxygenase Activity Cooperatively
Regulate Key Genes for Xenopus Eye and Neural
Development." Cell(Cambridge,Mass.),
151, 1200-1213. doi: 10.1016/j.cell.2012.11.014.
|
Crystal structure of tet3 in complex with a non-cpg
dsDNA . ➥(2) [+]:CcG/cGG, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, other-contacts
|
4lg7
|
hydrolase-DNA |
X-ray (2.5 Å) |
Xu C, Tempel W, Wernimont AK, Bountra C, Arrowsmith
CH, Edwards AM, Min J |
"Crystal structure MBD4 MBD domain in complex with
methylated CpG DNA." |
Crystal structure mbd4 mbd domain in complex with
methylated cpg DNA . ➥(2)
[+]:AcG/cGT,
[-]:cGT/AcG, is-WC-paired, is-in-duplex,
stacking-with-AA
|
4lt5
|
oxidoreductase-DNA |
X-ray (2.893 Å) |
Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N,
Correa IR, Zheng Y, Cheng X |
(2014) "Structure
of a Naegleria Tet-like dioxygenase in complex with
5-methylcytosine DNA." Nature,
506, 391-395. doi: 10.1038/nature12905.
|
Structure of a naegleria tet-like dioxygenase in
complex with 5-methylcytosine DNA . ➥(2) [+]:GcT/AGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
not-WC-paired, not-in-duplex, stacking-with-AA
|
4m9e
|
transcription-DNA |
X-ray (1.851 Å) |
Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H,
Blumenthal RM, Zhang X, Cheng X |
(2014) "Structural
basis for Klf4 recognition of methylated DNA."
Nucleic Acids Res., 42,
4859-4867. doi: 10.1093/nar/gku134.
|
Structure of klf4 zinc finger DNA binding domain in
complex with methylated DNA . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
4m9v
|
transcription-DNA |
X-ray (0.969 Å) |
Liu Y, Olanrewaju YO, Zhang X, Cheng X |
(2013) "DNA
recognition of 5-carboxylcytosine by a zfp57 mutant at
an atomic resolution of 0.97 angstrom."
Biochemistry, 52, 9310-9317.
doi: 10.1021/bi401360n.
|
Zfp57 mutant (e182q) in complex with 5-carboxylcytosine
DNA . ➥(2) [+]:CcG/cGG, is-WC-paired,
is-in-duplex, other-contacts
|
4mht
|
transferase-DNA |
X-ray (2.7 Å) |
O'Gara M, Klimasauskas S, Roberts RJ, Cheng X |
(1996) "Enzymatic
C5-cytosine methylation of DNA: mechanistic
implications of new crystal structures for HhaL
methyltransferase-DNA-AdoHcy complexes."
J.Mol.Biol., 261, 634-645.
doi: 10.1006/jmbi.1996.0489.
|
Ternary structure of hhai methyltransferase with native
DNA and adohcy . ➥(2) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
not-WC-paired, not-in-duplex, stacking-with-AA
|
4nm6
|
oxidoreductase-DNA |
X-ray (2.026 Å) |
Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG,
Zhu J, Wang P, Xu Y |
(2013) "Crystal
Structure of TET2-DNA Complex: Insight into
TET-Mediated 5mC Oxidation."
Cell(Cambridge,Mass.), 155,
1545-1555. doi: 10.1016/j.cell.2013.11.020.
|
Crystal structure of tet2-DNA complex . ➥(2) [-]:.GG/Cc., is-WC-paired,
is-in-duplex, not-WC-paired, not-in-duplex,
stacking-with-AA
|
4pw7
|
ligase-DNA |
X-ray (2.001 Å) |
Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu
RM |
(2014) "Structural
Basis for Hydroxymethylcytosine Recognition by the SRA
Domain of UHRF2." Mol.Cell,
54, 879-886. doi: 10.1016/j.molcel.2014.04.003.
|
Structure of uhrf2-sra in complex with a 5mc-containing
DNA . ➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
4qen
|
transcription-DNA |
X-ray (2.002 Å) |
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S,
Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel
DJ, Jacobsen SE |
(2014) "Mechanism
of DNA Methylation-Directed Histone Methylation by
KRYPTONITE." Mol.Cell,
55, 495-504. doi: 10.1016/j.molcel.2014.06.009.
|
Crystal structure of kryptonite in complex with mchh
DNA and sah . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
4qeo
|
transcription-DNA |
X-ray (2.0 Å) |
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S,
Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel
DJ, Jacobsen SE |
(2014) "Mechanism
of DNA Methylation-Directed Histone Methylation by
KRYPTONITE." Mol.Cell,
55, 495-504. doi: 10.1016/j.molcel.2014.06.009.
|
Crystal structure of kryptonite in complex with mchh
DNA, h3(1-15) peptide and sah . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
4qep
|
transcription-DNA |
X-ray (3.1 Å) |
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S,
Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel
DJ, Jacobsen SE |
(2014) "Mechanism
of DNA Methylation-Directed Histone Methylation by
KRYPTONITE." Mol.Cell,
55, 495-504. doi: 10.1016/j.molcel.2014.06.009.
|
Crystal structure of kryptonite in complex with mchg
DNA and sah . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
4r28
|
hydrolase-DNA |
X-ray (3.055 Å) |
Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ,
Zheng Y, Wilson GG, Cheng X |
(2014) "Modification-dependent
restriction endonuclease, MspJI, flips 5-methylcytosine
out of the DNA helix." Nucleic Acids Res.,
42, 12092-12101. doi: 10.1093/nar/gku871.
|
Mspji restriction endonuclease in complex with 27-mer
oligonucleotide . ➥(1)
not-WC-paired,
not-in-duplex, stacking-with-AA
|
4r2a
|
DNA binding protein-DNA |
X-ray (1.591 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Egr1-zif268 zinc fingers in complex with methylated DNA
. ➥(2) [+]:GcG/cGC, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
4r2e
|
DNA binding protein-DNA |
X-ray (1.84 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) zinc fingers in complex with
methylated DNA . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
4r2r
|
DNA binding protein-DNA |
X-ray (2.089 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) zinc fingers in complex with
carboxylated DNA . ➥(1)
[-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts
|
4r2s
|
DNA binding protein-DNA |
X-ray (2.489 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) q369p zinc fingers in complex
with methylated DNA . ➥(2)
[+]:GcG/cGC,
[-]:cGT/AcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
4x9j
|
transcription regulator-DNA |
X-ray (1.412 Å) |
Zandarashvili L, White MA, Esadze A, Iwahara J |
(2015) "Structural
impact of complete CpG methylation within target DNA on
specific complex formation of the inducible
transcription factor Egr-1." Febs Lett.,
589, 1748-1753. doi: 10.1016/j.febslet.2015.05.022.
|
Egr-1 with doubly methylated DNA . ➥(4) [+]:GcG/cGC, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
5bt2
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Chia JY, Tan WS, Ng CL, Hu NJ, Foo HL, Ho KL |
(2016) "A/T Run
Geometry of B-form DNA Is Independent of Bound
Methyl-CpG Binding Domain, Cytosine Methylation and
Flanking Sequence." Sci Rep,
6, 31210. doi: 10.1038/srep31210.
|
Mecp2 mbd domain (a140v) in complex with methylated DNA
. ➥(2) [+]:AcG/cGT, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
5cg9
|
oxidoreductase-DNA |
X-ray (2.693 Å) |
Hashimoto H, Pais JE, Dai N, Correa IR, Zhang X,
Zheng Y, Cheng X |
(2015) "Structure
of Naegleria Tet-like dioxygenase (NgTet1) in complexes
with a reaction intermediate 5-hydroxymethylcytosine
DNA." Nucleic Acids Res.,
43, 10713-10721. doi: 10.1093/nar/gkv870.
|
Ngtet1 in complex with 5mc DNA in space group p3221 .
➥(2) not-WC-paired, not-in-duplex,
stacking-with-AA
|
5cpj
|
"structural protein-DNA |
X-ray (3.15 Å) |
Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y,
Kurumizaka H |
(2015) "Influence
of DNA methylation on positioning and DNA flexibility
of nucleosomes with pericentric satellite DNA."
Open Biology, 5. doi:
10.1098/rsob.150128.
|
Nucleosome containing methylated sat2r DNA .
➥(2) [+]:TcG/cGA, [-]:cGA/TcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
other-contacts
|
5cpk
|
structural protein-DNA |
X-ray (2.632 Å) |
Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y,
Kurumizaka H |
(2015) "Influence
of DNA methylation on positioning and DNA flexibility
of nucleosomes with pericentric satellite DNA."
Open Biology, 5. doi:
10.1098/rsob.150128.
|
Nucleosome containing methylated sat2l DNA .
➥(1) [+]:TcG/cGA, is-WC-paired,
is-in-duplex, other-contacts
|
5ef6
|
transcription |
X-ray (3.0 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Structure of hoxb13 complex with methylated DNA .
➥(8) [+]:AcG/cGT, [-]:cGA/TcG,
[-]:cGG/CcG, hydrophobic-with-AA, is-WC-paired,
is-in-duplex
|
5ego
|
transcription |
X-ray (2.54 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Hoxb13-meis1 heterodimer bound to methylated DNA .
➥(2) [+]:AcG/cGT, [-]:cGA/TcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
5emc
|
transcription-DNA |
X-ray (2.3 Å) |
Jin J, Lian T, SU XD |
"The effects of cytosine methylation on general
transcription factors." |
Transcription factor grdbd and smgre complex .
➥(1) [-]:TGT/AcA, is-WC-paired,
is-in-duplex, other-contacts
|
5gse
|
structural protein-DNA |
X-ray (3.14 Å) |
Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi
N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J,
Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R,
Sugiyama M, Kurumizaka H |
(2017) "Crystal
structure of the overlapping dinucleosome composed of
hexasome and octasome." Science,
356, 205-208. doi: 10.1126/science.aak9867.
|
Crystal structure of unusual nucleosome . ➥(1) [+]:CcT/AGG, is-WC-paired,
is-in-duplex, other-contacts
|
5ke7
|
transcription-DNA |
X-ray (2.06 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 znf1-3 and tpg-mpa sequence DNA complex
structure . ➥(1) [-]:TGT/AcA, is-WC-paired,
is-in-duplex, other-contacts
|
5ke8
|
transcription-DNA |
X-ray (2.45 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 e446p znf1-3 and mpg-mpg sequence DNA
complex structure . ➥(2)
[+]:GcG/cGC,
[-]:cGT/AcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
5kl4
|
transcription-DNA |
X-ray (1.783 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4 q369h in complex with
formylated DNA . ➥(2) [-]:cGT/AcG, is-WC-paired,
is-in-duplex, other-contacts
|
5kl5
|
transcription-DNA |
X-ray (2.289 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4 q369h in complex with
carboxylated DNA . ➥(1)
[-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts
|
5kl7
|
transcription-DNA |
X-ray (1.579 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4q369r in complex with
carboxylated DNA . ➥(1)
[-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts
|
5lty
|
transcription |
X-ray (2.66 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Homeobox transcription factor cdx2 bound to methylated
DNA . ➥(2) [+]:AcG/cGT,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
5lux
|
transcription |
X-ray (3.23 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Homeobox transcription factor cdx1 bound to methylated
DNA . ➥(4) [+]:AcG/cGT, [-]:cGA/TcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
5mcv
|
transcription |
X-ray (1.6 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-lwc1) .
➥(4) [+]:gcG/Cgc, [-]:Cgc/gcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
5mcw
|
transcription |
X-ray (1.897 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-lwc2) .
➥(4) [+]:gcG/Cgc, [-]:Cgc/gcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
5mht
|
transferase-DNA |
X-ray (2.7 Å) |
O'Gara M, Roberts RJ, Cheng X |
(1996) "A
structural basis for the preferential binding of
hemimethylated DNA by HhaI DNA methyltransferase."
J.Mol.Biol., 263, 597-606.
doi: 10.1006/jmbi.1996.0601.
|
Ternary structure of hhai methyltransferase with
hemimethylated DNA and adohcy . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
5szx
|
transcription regulator-DNA |
X-ray (2.251 Å) |
Hong S, Wang D, Horton JR, Zhang X, Speck SH,
Blumenthal RM, Cheng X |
(2017) "Methyl-dependent
and spatial-specific DNA recognition by the orthologous
transcription factors human AP-1 and Epstein-Barr virus
Zta." Nucleic Acids Res.,
45, 2503-2515. doi: 10.1093/nar/gkx057.
|
Epstein-barr virus zta DNA binding domain homodimer in
complex with methylated DNA . ➥(2) [+]:TcG/cGA, [-]:cGC/GcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
5t00
|
transcription regulator-DNA |
X-ray (2.19 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Human ctcf znf3-7 and methylated DNA complex .
➥(4) [+]:GcG/cGC, [-]:cGC/GcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
5t01
|
transcription regulator-DNA |
X-ray (1.89 Å) |
Hong S, Wang D, Horton JR, Zhang X, Speck SH,
Blumenthal RM, Cheng X |
(2017) "Methyl-dependent
and spatial-specific DNA recognition by the orthologous
transcription factors human AP-1 and Epstein-Barr virus
Zta." Nucleic Acids Res.,
45, 2503-2515. doi: 10.1093/nar/gkx057.
|
Human c-jun DNA binding domain homodimer in complex
with methylated DNA . ➥(1)
[-]:CGT/AcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
5vmu
|
transcription-DNA |
X-ray (2.346 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a double cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . ➥(4) [+]:CcG/cGG, [+]:GcG/cGc,
[-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
5vmv
|
transcription-DNA |
X-ray (2.313 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with its double cpg-methylated DNA consensus
binding site . ➥(4) [+]:GcG/cGc, [+]:TcG/cGA,
[-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
5vmw
|
transcription-DNA |
X-ray (2.397 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a double cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . ➥(4) [+]:CcG/cGG, [+]:GcG/cGc,
[-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
5vmx
|
transcription-DNA |
X-ray (2.05 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a hemi cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . ➥(2) [+]:CcG/CGG, [+]:GcG/CGC,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
5vmy
|
transcription-DNA |
X-ray (2.002 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a hemi cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . ➥(2) [+]:CcG/CGG, [+]:GcG/CGC,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
5vmz
|
transcription-DNA |
X-ray (2.319 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) e535q mutant zinc finger DNA binding
domain in complex with a double cpg-methylated DNA
resembling the specific kaiso binding sequence (kbs) .
➥(4) [+]:CcG/cGG, [+]:GcG/cGc,
[-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
6a5n
|
gene regulation-DNA |
X-ray (2.4 Å) |
Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang
Z, Li S, Jacobsen SE, Du J |
(2018) "Mechanistic
insights into plant SUVH family H3K9 methyltransferases
and their binding to context-biased non-CG DNA
methylation." Proc. Natl. Acad. Sci.
U.S.A., 115, E8793-E8802. doi:
10.1073/pnas.1809841115.
|
Crystal structure of arabidopsis thaliana suvh6 in
complex with methylated DNA . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
6c1a
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with methylated DNA . ➥(2) [-]:TGT/AcA, is-WC-paired,
is-in-duplex, other-contacts
|
6c1t
|
DNA binding protein-DNA |
X-ray (1.84 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with a partially methylated DNA .
➥(1) [+]:AcA/TGT, is-WC-paired,
is-in-duplex, other-contacts
|
6c1u
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with a deoxy-oligonucleotide .
➥(2) [-]:TGT/AcA, is-WC-paired,
is-in-duplex, other-contacts
|
6c1y
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Lei M, Tempel W, Chen S, Liu K, Min J |
(2019) "Plasticity
at the DNA recognition site of the MeCP2 mCG-binding
domain." Biochim Biophys Acta Gene Regul
Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409.
|
Mbd of human mecp2 in complex with methylated DNA .
➥(4) [+]:CcG/cGG, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6c2f
|
DNA binding protein-DNA |
X-ray (2.65 Å) |
Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C,
Edwards AM, Min J, Structural Genomics Consortium |
"MBD2 in complex with methylated DNA." |
Mbd2 in complex with methylated DNA . ➥(6) [+]:CcG/CGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6cc8
|
DNA binding protein-DNA |
X-ray (1.95 Å) |
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J |
(2019) "Structural
analyses reveal that MBD3 is a methylated CG
binder." Febs J., 286,
3240-3254. doi: 10.1111/febs.14850.
|
Crystal structure mbd3 mbd domain in complex with
methylated cpg DNA . ➥(4)
[+]:AcG/cGT,
[-]:cGT/AcG, is-WC-paired, is-in-duplex,
stacking-with-AA
|
6ccg
|
transcription |
X-ray (1.9 Å) |
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J |
(2019) "Structural
analyses reveal that MBD3 is a methylated CG
binder." Febs J., 286,
3240-3254. doi: 10.1111/febs.14850.
|
Crystal structure mbd3 mbd domain in complex with
methylated cpg DNA . ➥(4)
[+]:GcG/cGC,
[-]:cGC/GcG, is-WC-paired, is-in-duplex,
stacking-with-AA
|
6ceu
|
transcription-DNA |
X-ray (2.005 Å) |
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J |
(2019) "Structural
analyses reveal that MBD3 is a methylated CG
binder." Febs J., 286,
3240-3254. doi: 10.1111/febs.14850.
|
Mbd3 mbd in complex with methylated, non-palindromic
cpg DNA: alternative interpretation of crystallographic
data . ➥(4) [+]:GcG/cGC, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6cnp
|
transcription-DNA |
X-ray (2.1 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Crystal structure of mbd2 complex with methylated cpg
island . ➥(4) [+]:CcG/cGG, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6cnq
|
transcription-DNA |
X-ray (2.151 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with methylated DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6d1t
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C,
Edwards AM, Min J, Structural Genomics Consortium |
"Complex of MBD1-MBD and methylated DNA." |
Complex of mbd1-mbd and methylated DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6e93
|
DNA binding protein-DNA |
X-ray (1.747 Å) |
Hudson NO, Whitby FG, Buck-Koehntop BA |
(2018) "Structural
insights into methylated DNA recognition by the
C-terminal zinc fingers of the DNA reader protein
ZBTB38." J. Biol. Chem.,
293, 19835-19843. doi: 10.1074/jbc.RA118.005147.
|
Crystal structure of zbtb38 c-terminal zinc fingers 6-9
in complex with methylated DNA . ➥(3) [+]:CcG/cGG, [+]:GcG/cGC,
[-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired,
is-in-duplex, other-contacts
|
6e94
|
DNA binding protein-DNA |
X-ray (1.594 Å) |
Hudson NO, Whitby FG, Buck-Koehntop BA |
(2018) "Structural
insights into methylated DNA recognition by the
C-terminal zinc fingers of the DNA reader protein
ZBTB38." J. Biol. Chem.,
293, 19835-19843. doi: 10.1074/jbc.RA118.005147.
|
Crystal structure of zbtb38 c-terminal zinc fingers 6-9
k1055r in complex with methylated DNA . ➥(3) [+]:CcG/cGG, [+]:GcG/cGC,
[-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired,
is-in-duplex, other-contacts, stacking-with-AA
|
6jnm
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu
F, Ma J, Cao X |
(2019) "DNA
methylation repels targeting of Arabidopsis REF6."
Nat Commun, 10, 2063. doi:
10.1038/s41467-019-10026-1.
|
Ref6 znf2-4-nac004-mc3 complex . ➥(2) [+]:TcT/AGA, [-]:AGA/TcT,
is-WC-paired, is-in-duplex, other-contacts
|
6jnn
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu
F, Ma J, Cao X |
(2019) "DNA
methylation repels targeting of Arabidopsis REF6."
Nat Commun, 10, 2063. doi:
10.1038/s41467-019-10026-1.
|
Ref6 znf2-4-nac004-mc1 complex . ➥(4) [+]:TcT/AGA, [-]:AGA/TcT,
is-WC-paired, is-in-duplex, other-contacts
|
6jtq
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Liu L, Yi C |
"RVD HA specifically contacts 5mC through van der
Waals interactions." |
Rvd ha specifically contacts 5mc through van der waals
interactions . ➥(2) [+]:TcG/CGA, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6jvz
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Rvd ha specifically contacts 5mc through van der waals
interactions . ➥(2) [+]:TcG/CGA, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6jw1
|
DNA binding protein-DNA |
X-ray (2.49 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Universal rvd r* accommodates 5mc via water-mediated
interactions . ➥(2) [+]:TcG/CGA, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6jw3
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Degenerate rvd rg forms a distinct loop conformation .
➥(4) [+]:TcG/CGA, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6lew
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Liu L, Yi C |
"RVD HA specifically contacts 5mC through van der
Waals interactions." |
Rvd ha specifically contacts 5mc through van der waals
interactions . ➥(2) [+]:TcG/CGA, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6m2v
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara
E |
(2021) "Mechanistic
insights into recognition of symmetric methylated
cytosines in CpG and non-CpG DNA by UHRF1 SRA."
Int.J.Biol.Macromol., 170,
514-522. doi: 10.1016/j.ijbiomac.2020.12.149.
|
Crystal structure of uhrf1 sra complexed with
fully-mchg DNA. . ➥(2)
not-WC-paired,
not-in-duplex, stacking-with-AA
|
6mg1
|
transcription-DNA |
X-ray (1.75 Å) |
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang
Y, Zhang X, Blumenthal RM, Cheng X |
(2019) "Structural
basis for effects of CpA modifications on C/EBP beta
binding of DNA." Nucleic Acids Res.,
47, 1774-1785. doi: 10.1093/nar/gky1264.
|
C-terminal bzip domain of human c-ebpbeta with 16bp
methylated oligonucleotide containing consensus
recognition sequence-c2 crystal form . ➥(4) [+]:GcA/TGc, [+]:GcG/cGc,
[-]:TGc/GcA, [-]:cGc/GcG, hydrophobic-with-AA,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6mg2
|
transcription-DNA |
X-ray (1.928 Å) |
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang
Y, Zhang X, Blumenthal RM, Cheng X |
(2019) "Structural
basis for effects of CpA modifications on C/EBP beta
binding of DNA." Nucleic Acids Res.,
47, 1774-1785. doi: 10.1093/nar/gky1264.
|
C-terminal bzip domain of human c-ebpbeta with 16bp
methylated oligonucleotide containing consensus
recognition sequence-c2221 crystal form . ➥(4) [+]:GcA/TGc, [+]:GcG/cGc,
[-]:TGc/GcA, [-]:cGc/GcG, hydrophobic-with-AA,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
6mg3
|
transcription-DNA |
X-ray (2.05 Å) |
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang
Y, Zhang X, Blumenthal RM, Cheng X |
(2019) "Structural
basis for effects of CpA modifications on C/EBP beta
binding of DNA." Nucleic Acids Res.,
47, 1774-1785. doi: 10.1093/nar/gky1264.
|
V285a mutant of the c-terminal bzip domain of human
c-ebpbeta with 16bp methylated oligonucleotide
containing consensus recognition sequence .
➥(4) [+]:GcA/TGc, [+]:GcG/cGc,
[-]:TGc/GcA, [-]:cGc/GcG, hydrophobic-with-AA,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
6mht
|
transferase-DNA |
X-ray (2.05 Å) |
Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ,
Cheng X |
(1997) "DNA
containing 4'-thio-2'-deoxycytidine inhibits
methylation by HhaI methyltransferase." Nucleic
Acids Res., 25, 2773-2783. doi:
10.1093/nar/25.14.2773.
|
Ternary structure of hhai methyltransferase with adohcy
and DNA containing 4'-thio-2'deoxycytidine at the
target . ➥(1) [+]:GcC/GGC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex
|
6ml6
|
transcription-DNA |
X-ray (1.54 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 4 with a cpa 5mc
modification) . ➥(1) [+]:GcA/TGC, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6ml7
|
transcription-DNA |
X-ray (1.75 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 4 with a cpg 5mc
modification) . ➥(1) [+]:AcG/CGT, is-WC-paired,
is-in-duplex, other-contacts
|
6ogk
|
DNA binding protein-DNA |
X-ray (1.65 Å) |
Lei M, Tempel W, Chen S, Liu K, Min J |
(2019) "Plasticity
at the DNA recognition site of the MeCP2 mCG-binding
domain." Biochim Biophys Acta Gene Regul
Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409.
|
Mecp2 mbd in complex with DNA . ➥(1) [+]:AcA/TGT, is-WC-paired,
is-in-duplex, other-contacts
|
6r64
|
hydrolase |
X-ray (2.64 Å) |
Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G,
Bochtler M |
(2019) "Crystal
structure of the EcoKMcrA N-terminal domain (NEco):
recognition of modified cytosine bases without
flipping." Nucleic Acids Res.,
47, 11943-11955. doi: 10.1093/nar/gkz1017.
|
N-terminal domain of modification dependent ecokmcra
restriction endonuclease (neco) in complex with c5mcgg
target sequence . ➥(4)
[+]:CcG/cGG,
[-]:cGG/CcG, hydrophobic-with-AA, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6t21
|
hydrolase |
X-ray (2.07 Å) |
Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G,
Bochtler M |
(2019) "Crystal
structure of the EcoKMcrA N-terminal domain (NEco):
recognition of modified cytosine bases without
flipping." Nucleic Acids Res.,
47, 11943-11955. doi: 10.1093/nar/gkz1017.
|
N-terminal domain of ecokmcra restriction endonuclease
(neco) in complex with t5mcga target sequence .
➥(4) [+]:TcG/cGA, [-]:cGA/TcG,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
stacking-with-AA
|
6w8v
|
transferase-DNA |
X-ray (3.12 Å) |
Adam S, Anteneh H, Hornisch M, Wagner V, Lu J, Radde
NE, Bashtrykov P, Song J, Jeltsch A |
(2020) "DNMT1 activity, base flipping mechanism and
genome-wide DNA methylation are regulated by the DNA
sequence context." Nat Commun. |
Crystal structure of mouse dnmt1 in complex with acg
DNA . ➥(2) [+]:Cc./.GG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6w8w
|
transferase-DNA |
X-ray (3.0 Å) |
Adam S, Anteneh H, Hornisch M, Wagner V, Lu J, Radde
NE, Bashtrykov P, Song J, Jeltsch A |
(2020) "DNMT1 activity, base flipping mechanism and
genome-wide DNA methylation are regulated by the DNA
sequence context." Nat Commun. |
Crystal structure of mouse dnmt1 in complex with ccg
DNA . ➥(2) [+]:Ac./.GT, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6x6e
|
DNA binding protein |
X-ray (2.0 Å) |
Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA |
(2021) "Structural
basis for glucocorticoid receptor recognition of both
unmodified and methylated binding sites, precursors of
a modern recognition element." Nucleic Acids
Res., 49, 8923-8933. doi:
10.1093/nar/gkab605.
|
Glucocorticoid receptor DNA binding domain in complex
with methylated precursor for a modern recognition
element (methylated pre-gbs) . ➥(2) [+]:GcG/CGC, [-]:CGG/CcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
6x9i
|
transferase |
X-ray (2.2 Å) |
Pappalardi MB, Keenan K, Cockerill M, Kellner WA,
Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel
M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso
N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin
RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler
JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE,
Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW,
Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X,
Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi
P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG,
Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin
SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM,
Waddell I, Kruger RG, McCabe MT |
(2021) "Discovery
of a first-in-class reversible DNMT1-selective
inhibitor with improved tolerability and efficacy in
acute myeloid leukemia." Nat Cancer,
2, 1002-1017.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA . ➥(1) [+]:CcC/GGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6x9j
|
transferase-transferase inhibitor-DNA |
X-ray (1.79 Å) |
Pappalardi MB, Keenan K, Cockerill M, Kellner WA,
Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel
M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso
N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin
RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler
JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE,
Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW,
Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X,
Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi
P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG,
Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin
SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM,
Waddell I, Kruger RG, McCabe MT |
(2021) "Discovery
of a first-in-class reversible DNMT1-selective
inhibitor with improved tolerability and efficacy in
acute myeloid leukemia." Nat Cancer,
2, 1002-1017.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and inhibitor gsk3830052 . ➥(1) [+]:CcG/uGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6x9k
|
transferase-transferase inhibitor-DNA |
X-ray (2.65 Å) |
Pappalardi MB, Keenan K, Cockerill M, Kellner WA,
Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel
M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso
N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin
RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler
JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE,
Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW,
Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X,
Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi
P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG,
Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin
SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM,
Waddell I, Kruger RG, McCabe MT |
(2021) "Discovery
of a first-in-class reversible DNMT1-selective
inhibitor with improved tolerability and efficacy in
acute myeloid leukemia." Nat Cancer,
2, 1002-1017.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and inhibitor gsk3685032a . ➥(1) [+]:CcG/uGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
6ykf
|
hydrolase |
X-ray (1.48 Å) |
Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz
T, Xu SY, Bochtler M |
(2021) "Crystal
structures of the EVE-HNH endonuclease VcaM4I in the
presence and absence of DNA." Nucleic Acids
Res., 49, 1708-1723. doi:
10.1093/nar/gkaa1218.
|
Vcam4i restriction endonuclease in the presence of
5mc-modified ssDNA . ➥(1)
not-WC-paired,
not-in-duplex, stacking-with-AA
|
6ymg
|
hydrolase |
X-ray (3.14 Å) |
Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz
T, Xu SY, Bochtler M |
(2021) "Crystal
structures of the EVE-HNH endonuclease VcaM4I in the
presence and absence of DNA." Nucleic Acids
Res., 49, 1708-1723. doi:
10.1093/nar/gkaa1218.
|
Vcam4i restriction endonuclease in complex with
5mc-modified dsDNA . ➥(2)
not-WC-paired,
not-in-duplex, stacking-with-AA
|
7cy6
|
transferase |
X-ray (2.1 Å) |
Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding
J |
(2021) "Molecular
mechanism for vitamin C-derived C 5
-glyceryl-methylcytosine DNA modification catalyzed by
algal TET homologue CMD1." Nat Commun,
12, 744. doi: 10.1038/s41467-021-21061-2.
|
Crystal structure of cmd1 in complex with 5mc-DNA .
➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
7cy8
|
transferase |
X-ray (2.4 Å) |
Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding
J |
(2021) "Molecular
mechanism for vitamin C-derived C 5
-glyceryl-methylcytosine DNA modification catalyzed by
algal TET homologue CMD1." Nat Commun,
12, 744. doi: 10.1038/s41467-021-21061-2.
|
Crystal structure of cmd1 in complex with 5mc-DNA and
vitamin c . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
7fef
|
DNA binding protein-DNA |
X-ray (2.39 Å) |
Wu Z, Chen S, Zhou M, Jia L, Li Z, Zhang X, Min J,
Liu K |
(2022) "Family-wide
Characterization of Methylated DNA Binding Ability of
Arabidopsis MBDs." J.Mol.Biol.,
434, 167404. doi: 10.1016/j.jmb.2021.167404.
|
Crystal structure of atmbd6 with DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
7mwk
|
DNA binding protein-DNA |
X-ray (2.453 Å) |
Liu K, Dong A, Edwards AM, Arrowsmith CH, Min J,
Structural Genomics Consortium (SGC) |
"Crystal structure of MBD2 with DNA." |
Crystal structure of mbd2 with DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
7mwm
|
DNA binding protein-DNA |
X-ray (1.601 Å) |
Liu K, Dong A, Edwards AM, Arrowsmith CH, Min J,
Structural Genomics Consortium (SGC) |
"Crystal structure of MBD2 with DNA." |
Crystal structure of mbd2 with DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
7ne3
|
oxidoreductase |
X-ray (2.26 Å) |
Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde
O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH,
Wojciechowski M, Razew M, Mayyas IM, Kardailsky O,
Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan
D, Jurkowska RZ, Krueger F, Plass C, Zacharias M,
Bochtler M, Hore TA, Jurkowski TP |
(2022) "Pronounced
sequence specificity of the TET enzyme catalytic domain
guides its cellular function." Sci Adv,
8, eabm2427. doi: 10.1126/sciadv.abm2427.
|
Human tet2 in complex with favourable DNA substrate. .
➥(2) [-]:.GT/Ac., is-WC-paired,
is-in-duplex, not-WC-paired, not-in-duplex,
stacking-with-AA
|
7ne6
|
oxidoreductase |
X-ray (2.3 Å) |
Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde
O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH,
Wojciechowski M, Razew M, Mayyas IM, Kardailsky O,
Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan
D, Jurkowska RZ, Krueger F, Plass C, Zacharias M,
Bochtler M, Hore TA, Jurkowski TP |
(2022) "Pronounced
sequence specificity of the TET enzyme catalytic domain
guides its cellular function." Sci Adv,
8, eabm2427. doi: 10.1126/sciadv.abm2427.
|
Human tet2 in complex with unfavourable DNA substrate.
. ➥(2) [-]:.GC/Gc., is-WC-paired,
is-in-duplex, not-WC-paired, not-in-duplex,
stacking-with-AA
|
7nx5
|
viral protein |
X-ray (2.5 Å) |
Bernaudat F, Gustems M, Gunther J, Oliva MF, Buschle
A, Gobel C, Pagniez P, Lupo J, Signor L, Muller CW,
Morand P, Sattler M, Hammerschmidt W, Petosa C |
(2022) "Structural
basis of DNA methylation-dependent site selectivity of
the Epstein-Barr virus lytic switch protein
ZEBRA/Zta/BZLF1." Nucleic Acids Res.,
50, 490-511. doi: 10.1093/nar/gkab1183.
|
Crystal structure of the epstein-barr virus protein
zebra (bzlf1, zta) bound to a methylated DNA duplex .
➥(3) [+]:TcG/cGA, [-]:cGC/GcG,
is-WC-paired, is-in-duplex, other-contacts,
stacking-with-AA
|
7r77
|
transferase-DNA |
cryo-EM (3.0 Å) |
Wang J, Catania S, Wang C, de la Cruz MJ, Rao B,
Madhani HD, Patel DJ |
(2022) "Structural
insights into DNMT5-mediated ATP-dependent
high-fidelity epigenome maintenance."
Mol.Cell, 82, 1186-1198.e6.
doi: 10.1016/j.molcel.2022.01.028.
|
cryo-EM structure of dnmt5 binary complex with
hemimethylated DNA . ➥(1)
[+]:GcC/GGC,
is-WC-paired, is-in-duplex, other-contacts
|
7r78
|
transferase-DNA |
cryo-EM (3.5 Å) |
Wang J, Catania S, Wang C, de la Cruz MJ, Rao B,
Madhani HD, Patel DJ |
(2022) "Structural
insights into DNMT5-mediated ATP-dependent
high-fidelity epigenome maintenance."
Mol.Cell, 82, 1186-1198.e6.
doi: 10.1016/j.molcel.2022.01.028.
|
cryo-EM structure of dnmt5 quaternary complex with
hemimethylated DNA, amp-pnp and sah . ➥(1) [+]:Gc./.GC, is-WC-paired,
is-in-duplex, other-contacts
|
7ray
|
DNA binding protein-DNA |
X-ray (1.78 Å) |
Liu K, Dong A, Loppnau P, Edwards AM, Arrowsmith CH,
Min J, Structural Genomics Consortium (SGC) |
"Crystal structure of MBD2 with DNA." |
Crystal structure of mbd2 with DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG,
is-WC-paired, is-in-duplex, stacking-with-AA
|
7sfc
|
transferase-transferase inhibitor |
X-ray (1.97 Å) |
Horton JR, Pathuri S, Wong K, Ren R, Rueda L,
Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB,
Zhang X, King BW, Cheng X |
(2022) "Structural
characterization of dicyanopyridine containing
DNMT1-selective, non-nucleoside inhibitors."
Structure, 30, 793-802.e5.
doi: 10.1016/j.str.2022.03.009.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and inhibitor gsk3735967a . ➥(1) [+]:CcG/uGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7sfd
|
transferase-transferase inhibitor |
X-ray (2.09 Å) |
Horton JR, Pathuri S, Wong K, Ren R, Rueda L,
Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB,
Zhang X, King BW, Cheng X |
(2022) "Structural
characterization of dicyanopyridine containing
DNMT1-selective, non-nucleoside inhibitors."
Structure, 30, 793-802.e5.
doi: 10.1016/j.str.2022.03.009.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and inhibitor gsk3543105a . ➥(1) [+]:CcG/uGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7sfe
|
transferase-transferase inhibitor |
X-ray (2.55 Å) |
Horton JR, Pathuri S, Wong K, Ren R, Rueda L,
Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB,
Zhang X, King BW, Cheng X |
(2022) "Structural
characterization of dicyanopyridine containing
DNMT1-selective, non-nucleoside inhibitors."
Structure, 30, 793-802.e5.
doi: 10.1016/j.str.2022.03.009.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and inhibitor gsk3830334a . ➥(1) [+]:CcG/uGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7sff
|
transferase-transferase inhibitor |
X-ray (2.05 Å) |
Horton JR, Pathuri S, Wong K, Ren R, Rueda L,
Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB,
Zhang X, King BW, Cheng X |
(2022) "Structural
characterization of dicyanopyridine containing
DNMT1-selective, non-nucleoside inhibitors."
Structure, 30, 793-802.e5.
doi: 10.1016/j.str.2022.03.009.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and inhibitor gsk3852279b . ➥(1) [+]:CcG/uGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7sfg
|
transferase-transferase inhibitor |
X-ray (2.43 Å) |
Horton JR, Pathuri S, Wong K, Ren R, Rueda L,
Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB,
Zhang X, King BW, Cheng X |
(2022) "Structural
characterization of dicyanopyridine containing
DNMT1-selective, non-nucleoside inhibitors."
Structure, 30, 793-802.e5.
doi: 10.1016/j.str.2022.03.009.
|
Human dnmt1(729-1600) bound to zebularine-containing
12mer dsDNA and cofactor sam . ➥(1) [+]:CcC/GGG, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7t02
|
transferase-DNA |
cryo-EM (3.8 Å) |
Wang J, Catania S, Wang C, de la Cruz MJ, Rao B,
Madhani HD, Patel DJ |
(2022) "Structural
insights into DNMT5-mediated ATP-dependent
high-fidelity epigenome maintenance."
Mol.Cell, 82, 1186-1198.e6.
doi: 10.1016/j.molcel.2022.01.028.
|
cryo-EM structure of dnmt5 pseudo-ternary complex
solved by incubation with hemimethylated DNA and sam .
➥(1) [+]:Gc./.GC, is-WC-paired,
is-in-duplex, other-contacts
|
7xi9
|
transferase-DNA |
cryo-EM (2.52 Å) |
Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S,
Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A,
Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A,
Nakanishi M, Defossez PA, Arita K |
(2022) "Structural
basis for activation of DNMT1." Nat
Commun, 13, 7130. doi: 10.1038/s41467-022-34779-4.
|
cryo-EM structure of human dnmt1 (aa:351-1616) in
complex with ubiquitinated h3 and hemimethylated DNA
analog (cxxc-ordered form) . ➥(1) [+]:Ac./.GT, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7xib
|
transferase-DNA |
cryo-EM (2.23 Å) |
Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S,
Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A,
Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A,
Nakanishi M, Defossez PA, Arita K |
(2022) "Structural
basis for activation of DNMT1." Nat
Commun, 13, 7130. doi: 10.1038/s41467-022-34779-4.
|
cryo-EM structure of human dnmt1 (aa:351-1616) in
complex with ubiquitinated h3 and hemimethylated DNA
analog (cxxc-disordered form) . ➥(1) [+]:Ac./.GT, is-WC-paired,
is-in-duplex, stacking-with-AA
|
7yhp
|
DNA binding protein-DNA |
cryo-EM (3.1 Å) |
Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M,
Li S, Zhu JK, Du J |
(2023) "Molecular
basis of the plant ROS1-mediated active DNA
demethylation." Nat.Plants,
9, 271-279. doi: 10.1038/s41477-022-01322-8.
|
Cryoem structure of arabidopsis ros1 in complex with
5mc-dsDNA at 3.1 angstroms resolution . ➥(1) hydrophobic-with-AA,
not-WC-paired, not-in-duplex
|
7yun
|
DNA binding protein |
X-ray (2.13 Å) |
Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y,
Hughes TR, Min J |
(2023) "Structural
insights into DNA recognition by the BEN domain of the
transcription factor BANP." J.Biol.Chem.,
299, 104734. doi: 10.1016/j.jbc.2023.104734.
|
Crystal structure of human bend6 ben domain in complex
with methylated DNA . ➥(2)
[+]:GcG/CGc,
[-]:CGc/GcG, is-WC-paired, is-in-duplex,
other-contacts, stacking-with-AA
|
8c56
|
transferase |
X-ray (2.4 Å) |
Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D,
Bochtler M |
(2024) "Cytosine
analogues as DNA methyltransferase substrates."
Nucleic Acids Res., 52,
9267-9281. doi: 10.1093/nar/gkae568.
|
Cpg specific m.mpei methyltransferase crystallized in
the presence of 2'-deoxy-5-methylzebularine (5mz) and
5-methylcytosine containing dsDNA . ➥(1) [-]:GGC/GcC, is-WC-paired,
is-in-duplex, stacking-with-AA
|
8c57
|
transferase |
X-ray (1.95 Å) |
Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D,
Bochtler M |
(2024) "Cytosine
analogues as DNA methyltransferase substrates."
Nucleic Acids Res., 52,
9267-9281. doi: 10.1093/nar/gkae568.
|
Cpg specific m.mpei methyltransferase crystallized in
the presence of 5,6-dihydro-5-azacytosine (converted to
5m-dhac) and 5-methylcytosine containing dsDNA .
➥(1) [-]:GGC/GcC, is-WC-paired,
is-in-duplex, stacking-with-AA
|
8c58
|
transferase |
X-ray (1.85 Å) |
Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D,
Bochtler M |
(2024) "Cytosine
analogues as DNA methyltransferase substrates."
Nucleic Acids Res., 52,
9267-9281. doi: 10.1093/nar/gkae568.
|
Cpg specific m.mpei methyltransferase crystallized in
the presence of 5-hydroxycytosine and 5-methylcytosine
containing dsDNA . ➥(1)
[-]:GGC/GcC,
is-WC-paired, is-in-duplex, stacking-with-AA
|
8c59
|
transferase |
X-ray (1.7 Å) |
Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D,
Bochtler M |
(2024) "Cytosine
analogues as DNA methyltransferase substrates."
Nucleic Acids Res., 52,
9267-9281. doi: 10.1093/nar/gkae568.
|
Cpg specific m.mpei methyltransferase crystallized in
the presence of 5-bromocytosine (converted to 5mc) and
5-methylcytosine containing dsDNA . ➥(2) [-]:GGC/GcC,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
not-WC-paired, not-in-duplex, stacking-with-AA
|
8eng
|
transcription-DNA |
X-ray (1.25 Å) |
Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN,
Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon
GMK |
(2023) "DNA
selection by the master transcription factor PU.1."
Cell Rep, 42, 112671. doi:
10.1016/j.celrep.2023.112671.
|
Human pu.1 ets-domain (165-270) bound to
d(aataagcggaagtggg) with hemi-methylated cpg (forward
strand) . ➥(1) [+]:GcG/CGC, is-WC-paired,
is-in-duplex, other-contacts
|
8eo1
|
transcription-DNA |
X-ray (1.28 Å) |
Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN,
Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon
GMK |
(2023) "DNA
selection by the master transcription factor PU.1."
Cell Rep, 42, 112671. doi:
10.1016/j.celrep.2023.112671.
|
Human pu.1 ets-domain (165-270) bound to
d(aataagcggaagtggg) with hemi-methylated cpg (reverse
strand) . ➥(1) [-]:CGG/CcG, is-WC-paired,
is-in-duplex, other-contacts
|
8eo4
|
transcription-DNA |
X-ray (1.24 Å) |
Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN,
Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon
GMK |
(2023) "DNA
selection by the master transcription factor PU.1."
Cell Rep, 42, 112671. doi:
10.1016/j.celrep.2023.112671.
|
Human pu.1 ets-domain (165-270) bound to
d(aataagcggaagtggg) with di-methylated cpg sites .
➥(2) [+]:GcG/cGC, [-]:cGG/CcG,
is-WC-paired, is-in-duplex, other-contacts
|
8htx
|
DNA binding protein |
X-ray (2.8 Å) |
Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y,
Hughes TR, Min J |
(2023) "Structural
insights into DNA recognition by the BEN domain of the
transcription factor BANP." J.Biol.Chem.,
299, 104734. doi: 10.1016/j.jbc.2023.104734.
|
Crystal structure of banp in complex with methylated
DNA . ➥(4) [+]:TcG/CGA, [-]:CGA/TcG,
is-WC-paired, is-in-duplex, other-contacts
|
8ik4
|
DNA binding protein |
X-ray (2.1 Å) |
Adhav VA, Saikrishnan K |
"Structural basis of target recognition by the DNA
binding domain of McrBC." |
Structure of DNA binding domain of mcrbc endonuclease
bound to hemimethylated DNA: l68f mutant . ➥(1) not-WC-paired, not-in-duplex,
stacking-with-AA
|
8jkk
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Zhang L, Mu Y, Li T, Hu J, Lin H, Zhang L |
(2024) "Molecular
basis of an atypical dsDNA 5mC/6mA bifunctional
dioxygenase CcTet from Coprinopsis cinerea in
catalyzing dsDNA 5mC demethylation." Nucleic
Acids Res., 52, 3886-3895. doi:
10.1093/nar/gkae066.
|
Crystal structure of the dioxygenase cctet from
coprinopsis cinerea bound to 12bp 5-methylcytosine
(5mc) containing duplex DNA . ➥(4) not-WC-paired, not-in-duplex,
stacking-with-AA
|
8q5o
|
hydrolase |
X-ray (2.33 Å) |
Szafran K, Rafalski D, Skowronek K, Wojciechowski M,
Kazrani AA, Gilski M, Xu SY, Bochtler M |
(2024) "Structural
analysis of the BisI family of modification dependent
restriction endonucleases." Nucleic Acids
Res., 52, 9103-9118. doi:
10.1093/nar/gkae634.
|
N-terminal domain of restriction endonuclease eco15i
with tetra-methylated target DNA. . ➥(4) [+]:GcT/AGc, [-]:TGc/GcA,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
stacking-with-AA
|
8rpx
|
hydrolase |
X-ray (1.81 Å) |
Szafran K, Rafalski D, Skowronek K, Wojciechowski M,
Kazrani AA, Gilski M, Xu SY, Bochtler M |
(2024) "Structural
analysis of the BisI family of modification dependent
restriction endonucleases." Nucleic Acids
Res., 52, 9103-9118. doi:
10.1093/nar/gkae634.
|
Nhoi restriction endonuclease in complex with quadruply
methylated DNA target . ➥(10)
[+]:GcA/TGc,
[+]:GcT/AGc, [-]:AGc/GcT, [-]:TGc/GcA,
hydrophobic-with-AA, is-WC-paired, is-in-duplex,
not-WC-paired, not-in-duplex, other-contacts,
stacking-with-AA
|
8tlk
|
DNA binding protein-DNA |
X-ray (2.99 Å) |
Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu
B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T |
(2023) "The ICF
syndrome protein CDCA7 harbors a unique DNA-binding
domain that recognizes a CpG dyad in the context of a
non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946.
|
Cdca7 (human) binds non-b-form 32-mer DNA oligo
containing a 5mc . ➥(2)
[+]:TcG/CGT,
[-]:CGT/TcG, is-WC-paired, is-in-duplex,
stacking-with-AA
|
8xp8
|
DNA-antibiotic |
X-ray (1.64 Å) |
Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang
CK, Chou SH, Neidle S, Hou MH |
(2024) "Structural
basis of water-mediated cis Watson-Crick/Hoogsteen
base-pair formation in non-CpG methylation."
Nucleic Acids Res., 52,
8566-8579. doi: 10.1093/nar/gkae594.
|
Crystal structure of d(acgmccgt-acggcgt) in complex
with echinomycin . ➥(1)
[-]:GGC/GcC,
is-WC-paired, is-in-duplex, other-contacts
|
8xqc
|
transferase |
cryo-EM (3.25 Å) |
Hayashi G, Takahashi Y, Kikuchi A, Kori S, Arita K,
Murakami H |
"Activation of DNMT1 by Chemically Synthesized Dual
monoubiquitinated PAF15 Protein." |
cryo-EM structure of human dnmt1 (aa:351-1616) in
complex with ubiquitinated paf15 and hemimethylated DNA
analog . ➥(1) [+]:Ac./.GT, is-WC-paired,
is-in-duplex, stacking-with-AA
|
8yv8
|
DNA binding protein |
cryo-EM (3.0 Å) |
Wassing I, Nishiyama A, Arita K, Funabiki H |
"CDCA7 is a hemimethylated DNA adaptor for the
nucleosome remodeler HELLS." |
cryo-EM structure of cdca7 bound to nucleosome
including hemimethylated cpg site in widom601
positioning sequence. . ➥(1)
[+]:TcG/CGA,
is-WC-paired, is-in-duplex, stacking-with-AA
|