6CEU: MBD3 MBD

MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 May 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 2,146
Mol. weight: 31.66 kDa
Released: 9 May 2018

Explore 6CEU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CEU contains 2 α-helices and 14 β-strands across 2 chains. 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: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	16-21	6	1
β-strand	25	1	2
β-strand	31-36	6	1
β-strand	42-43	2	1
α-helix	46-53	8
β-strand	62-63	2	3
β-strand	68-69	2	3

Chain B: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	16-21	6	4
β-strand	24	1	2
β-strand	31-36	6	4
β-strand	42-43	2	4
α-helix	46-53	8
β-strand	62-63	2	5
β-strand	68-69	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Methyl-CpG-binding domain protein 3	A, B	protein	73	Homo sapiens	O95983 (AlphaFold model)
DNA (5'-D(GPCPCPAPGP(5CM)PGPTPTPGPGPC)-3')	C, E	DNA	12	synthetic construct
DNA (5'-D(GPCPCPAPAP(5CM)PGPCPTPGPGPC)-3')	D, F	DNA	12	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6CEU_1 Methyl-CpG-binding domain protein 3 (chains A, B)
GSMERKRWECPALPQGWEREEVPRRSGLSAGHRDVFYYSPSGKKFRSKPQLARYLGGSMD
LSTFDFRTGKMLM

Sequence of entity 2 (C, E), FASTA

>6CEU_2 DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3') (chains C, E)
GCCAGCGTTGGC

Sequence of entity 3 (D, F), FASTA

>6CEU_3 DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3') (chains D, F)
GCCAACGCTGGC

Primary citation

Structural analyses reveal that MBD3 is a methylated CG binder. Liu, K., Lei, M., Wu, Z. et al. FEBS J (2019) 286:3240-3254. DOI 10.1111/febs.14850 · 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
6CEV 2.0 Å, MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation…
2MB7 Solution structure of MBD3 methylcytosine binding domain
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 6CEU 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.