5mC interactions in PDB entry 3C2I auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

PDB-id

3C2I

Class

transcription regulator

Method

X-ray (2.5 Å)

Summary

The crystal structure of methyl-cpg binding domain of human mecp2 in complex with a methylated DNA sequence from bdnf
List of 2 5mC-amino acid contacts:

B.5CM8: stacking-with-A.ARG111 is-WC-paired is-in-duplex [+]:AcG/cGT

C.5CM33: stacking-with-A.ARG133 is-WC-paired is-in-duplex [-]:cGG/CcG

direct SNAP output · DNAproDB 2.0

Reference

Ho, K.L., McNae, I.W., Schmiedeberg, L., Klose, R.J., Bird, A.P., Walkinshaw, M.D.: (2008) "MeCP2 binding to DNA depends upon hydration at methyl-CpG." Mol.Cell, 29, 525-531.

Abstract

MeCP2 is an essential transcriptional repressor that mediates gene silencing through binding to methylated DNA. Binding specificity has been thought to depend on hydrophobic interactions between cytosine methyl groups and a hydrophobic patch within the methyl-CpG-binding domain (MBD). X-ray analysis of a methylated DNA-MBD cocrystal reveals, however, that the methyl groups make contact with a predominantly hydrophilic surface that includes tightly bound water molecules. This suggests that MeCP2 recognizes hydration of the major groove of methylated DNA rather than cytosine methylation per se. The MeCP2-DNA complex also identifies a unique structural role for T158, the residue most commonly mutated in Rett syndrome.

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model, with the methyl-carbon atom in black.
Watson-Crick base pairs are represented as long rectangular blocks with the minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code by chain identifier.
The block schematics were created with 3DNA-DSSR, and images were rendered using PyMOL.
Download the PyMOL session file corresponding to the top-left image in the following panel.

List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

The contacts include paired nucleotides (mostly a G in G-C pairing), and amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
The structure is oriented in the 'standard' 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.

	No. 1 B.5CM8: download PDB file for the 5mC entry stacking-with-A.ARG111 is-WC-paired is-in-duplex [+]:AcG/cGT
	No. 2 C.5CM33: download PDB file for the 5mC entry stacking-with-A.ARG133 is-WC-paired is-in-duplex [-]:cGG/CcG