2MB7: MBD3 methylcytosine binding domain

Solution structure of MBD3 methylcytosine binding domain. Determined by solution NMR. Released 11 Dec 2013.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 584
Mol. weight: 8.34 kDa
Released: 11 Dec 2013

Explore 2MB7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2MB7 contains 2 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
α-helix	14	1
β-strand	15	1	2
β-strand	17	1	2
β-strand	18-26	9	1
β-strand	29-38	10	1
β-strand	44-45	2	1
α-helix	48-55	8
β-strand	65	1	3
β-strand	70	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Methyl-CpG-binding domain protein 3	A	protein	72	Homo sapiens	O95983 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2MB7_1 Methyl-CpG-binding domain protein 3 (chains A)
GSMERKRWECPALPQGWEREEVPRRSGLSAGHRDVFYYSPSGKKFRSKPQLARYLGGSMD
LSTFDFRTGKML

Primary citation

Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA. Cramer, J.M., Scarsdale, J.N., Walavalkar, N.M. et al. J Biol Chem (2014) 289:1294-1302. DOI 10.1074/jbc.M113.512236 · PubMed

Other PDB entries of the same protein (UniProt O95983 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CCG 1.9 Å, Crystal structure MBD3 MBD domain in complex with methylated CpG DNA
6CC8 1.95 Å, Crystal structure MBD3 MBD domain in complex with methylated CpG DNA
6CEU 2.0 Å, MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation…
6CEV 2.0 Å, MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation…
9A2A Integrative structure of the human MHM complex
9A2C Integrative structure of the human NuDe complex
9A8O Integrative structure of the NuRD corepressor complex
9AAX Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome

Browse structure collections

About this viewer

MolViewer shows 2MB7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.