SNAP-annotated 5mC-DNA-protein interactions: PDB entry 9ogr

PDB-id

9ogr; DSSR-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein

Method

cryo-EM (2.78 Å)

Summary

cryo-EM analysis of human h2a.z on methylated sat2r-p DNA (v1)

Reference

Shih RM, Arimura Y, Konishi HA, Funabiki H (2026): "Impacts of DNA methylation on H2A.Z deposition and nucleosome stability." Elife. doi: 10.7554/elife.109762.2.

Abstract

 

• 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.