› 6kdl

X-ray diffraction
3.27Å resolution

Crystal structure of human DNMT3B-DNMT3L complex (I)

Released:
DOI: 10.2210/pdb6kdl/pdb
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PDB entry 6kdl coloured by chain, front view.
PDB entry 6kdl coloured by chain, side view.
PDB entry 6kdl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS
OpenAccess logo Nucleic Acids Res 48 3949-3961 (2020)
PMID: 32083663

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193644 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA (cytosine-5)-methyltransferase 3B Chains: A, D
Molecule details ›
Chains: A, D
Length: 286 amino acids
Theoretical weight: 32.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBC3 (Residues: 571-853; Coverage: 33%)
Gene name: DNMT3B
Sequence domains: C-5 cytosine-specific DNA methylase
DNA (cytosine-5)-methyltransferase 3-like Chains: B, C
Molecule details ›
Chains: B, C
Length: 204 amino acids
Theoretical weight: 23.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UJW3 (Residues: 178-379; Coverage: 52%)
  • Best match: Q9UJW3-2 (Residues: 178-380)
Gene name: DNMT3L

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P31
Unit cell:
a: 192.932Å b: 192.932Å c: 50.041Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.179 0.212
Expression system: Escherichia coli

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Citations

6 review citations

DNMTs and Impact of CpG Content, Transcription Factors, Consensus Motifs, lncRNAs, and Histone Marks on DNA Methylation.
Loaeza-Loaeza et al. (2020)
5 more

3 mentions without citation

Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Lin et al. (2020)
2 more

PDB-REDO

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