SNAP output for PDB entry 5ybd [SNAP web server]

PDB-id

5ybd; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein

Method

X-ray (2.769 Å)

Summary

X-ray structure of ets domain of ergp55 in complex with e74DNA

Reference

Sharma R, Gangwar SP, Saxena AK (2018): "Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence." Acta Crystallogr F Struct Biol Commun, 74, 656-663. doi: 10.1107/S2053230X1801110X.

Abstract

ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P4₁2₁2 and of its complex with the E74 DNA sequence (DNA₉) in space group C222₁ were obtained and their structures were determined. Comparative structure analysis of the ETSi domain and its complex with DNA₉ with previously determined structures of the ERGi domain (the ETS domain of ERG containing inhibitory motifs) in space group P6₅2₁2 and of the ERGi-DNA₁₂ complex in space group P4₁2₁2 were performed. The ETSi domain is observed as a homodimer in solution as well as in the crystallographic asymmetric unit. Superposition of the structure of the ETSi domain on that of the ERGi domain showed a major conformational change at the C-terminal DNA-binding autoinhibitory (CID) motif, while minor changes are observed in the loop regions of the ETSi-domain structure. The ETSi-DNA₉ complex in space group C222₁ forms a structure that is quite similar to that of the ERG-DNA₁₂ complex in space group P4₁2₁2. Upon superposition of the complexes, major conformational changes are observed at the 5' and 3' ends of DNA₉, while the conformation of the core GGA nucleotides was quite conserved. Comparison of the ETSi-DNA₉ structure with known structures of ETS class 1 protein-DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.