6CNP: MBD2 complex with methylated CpG island

Crystal structure of MBD2 complex with methylated CpG island. Determined by X-ray diffraction at 2.1 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 1,968
Mol. weight: 36.62 kDa
Ligands: CA
Released: 28 Mar 2018

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

Secondary structure: helices and β-sheets

6CNP contains 3 α-helices and 9 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, 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
β-strand	206-207	2	2
β-strand	212-213	2	2

Chain B: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	155-156	2
β-strand	160-165	6	3
β-strand	175-180	6	3
β-strand	186-187	2	3
α-helix	190-197	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Methyl-CpG-binding domain protein 2	A, B	protein	96	Homo sapiens	Q9UBB5 (AlphaFold model)
DNA (5'-D(GPCPCPAPCP(5CM)PGPGPTPGPGPC)-3')	C, D, E, F	DNA	12	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6CNP_1 Methyl-CpG-binding domain protein 2 (chains A, B)
MHHHHHHSSGRENLYFQGATESGKRMDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSG
KKFRSKPQLARYLGNTVDLSSFDFRTGKMMPSKLQK

Sequence of entity 2 (C, D, E, F), FASTA

>6CNP_2 DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3') (chains C, D, E, F)
GCCACCGGTGGC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (UNX) are not listed.

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
6CNQ 2.15 Å, MBD2 in complex with methylated DNA
6C1U 2.3 Å, MBD2 in complex with a deoxy-oligonucleotide
6C1V 2.3 Å, MBD2 in complex with double-stranded DNA
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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