6C1V: MBD2

MBD2 in complex with double-stranded DNA. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Feb 2018.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 3,061
Mol. weight: 327.09 kDa
Released: 14 Feb 2018

Explore 6C1V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C1V contains 9 α-helices and 24 β-strands across 4 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.

Chains A and E: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	150-151	2	1
β-strand	160-165	6	1
β-strand	175-180	6	1
β-strand	186-187	2	1
α-helix	190-197	8
α-helix	198-200	3
β-strand	206-207	2	2
β-strand	212-213	2	2

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	150-151	2	3
β-strand	160-165	6	3
β-strand	175-180	6	3
β-strand	186-187	2	3
α-helix	190-197	8
α-helix	198-200	3
β-strand	207	1	4
β-strand	212	1	4

Chain F: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	150-151	2	7
α-helix	156	1
β-strand	160-165	6	7
β-strand	175-180	6	7
β-strand	186-187	2	7
α-helix	190-197	8
α-helix	198-200	3
β-strand	206-207	2	8
β-strand	212-213	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Methyl-CpG-binding domain protein 2	A, B, E, F	protein	79	Homo sapiens	Q9UBB5 (AlphaFold model)
12-mer DNA	C, G	DNA	12	synthetic construct
12-mer DNA	D, H	DNA	12	synthetic construct

Sequence of entity 1 (A, B, E, F), FASTA

>6C1V_1 Methyl-CpG-binding domain protein 2 (chains A, B, E, F)
GATESGKRMDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNTV
DLSSFDFRTGKMMPSKLQK

Sequence of entity 2 (C, G), FASTA

>6C1V_2 12-mer DNA (chains C, G)
CGGAGTGTAGGC

Sequence of entity 3 (D, H), FASTA

>6C1V_3 12-mer DNA (chains D, H)
GCCTACACTCCG

Primary citation

Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA. Liu, K., Xu, C., Lei, M. et al. J Biol Chem (2018) 293:7344-7354. DOI 10.1074/jbc.RA118.001785 · PubMed

Other PDB entries of the same protein (UniProt Q9UBB5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MWM 1.6 Å, Crystal structure of MBD2 with DNA
7RAY 1.78 Å, Crystal structure of MBD2 with DNA
6C1T 1.84 Å, MBD2 in complex with a partially methylated DNA
6C1A 2.05 Å, MBD2 in complex with methylated DNA
6CNP 2.1 Å, Crystal structure of MBD2 complex with methylated CpG island
6CNQ 2.15 Å, MBD2 in complex with methylated DNA
6C1U 2.3 Å, MBD2 in complex with a deoxy-oligonucleotide
7MWK 2.45 Å, Crystal structure of MBD2 with DNA
6C2F 2.65 Å, MBD2 in complex with methylated DNA
7AO8 4.5 Å, Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex
7AO9 6.1 Å, Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex
7AOA 19.4 Å, Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex

Browse structure collections

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