SNAP-annotated 5mC-DNA-protein interactions: PDB entry 5t00

PDB-id

5t00; DSSR-derived features in text and JSON formats; DNAproDB

Class

transcription regulator-DNA

Method

X-ray (2.19 Å)

Summary

Human ctcf znf3-7 and methylated DNA complex

Reference

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.

Abstract

The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3-7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.

• The contacts include paired nucleotides (mostly a G in Watson-Crick G-C pairing) and amino-acids within a 4.5-Å distance cutoff to base atoms of 5mC.
• The structure is oriented in the base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
• The black sphere (•) denotes the 5-methyl carbon atom in 5mC.