› 6k3a

X-ray diffraction
2.3Å resolution

Crystal structure of human PCNA in complex with DNMT1 PIP box motif.

Released:
DOI: 10.2210/pdb6k3a/pdb
PDB entry 6k3a coloured by chain, front view.
PDB entry 6k3a coloured by chain, side view.
PDB entry 6k3a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction.
Jimenji T, Matsumura R, Kori S, Arita K
Biochem Biophys Res Commun 516 578-583 (2019)
PMID: 31235252

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146043 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Proliferating cell nuclear antigen Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 264 amino acids
Theoretical weight: 29.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P12004 (Residues: 1-261; Coverage: 100%)
Gene name: PCNA
Sequence domains:
DNA (cytosine-5)-methyltransferase 1 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 20 amino acids
Theoretical weight: 2.22 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P26358 (Residues: 161-180; Coverage: 1%)
Gene names: AIM, CXXC9, DNMT, DNMT1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2
Unit cell:
a: 141.54Å b: 81.598Å c: 68.105Å
α: 90° β: 90.02° γ: 90°
R-values:
R R work R free
0.22 0.217 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Regulatory mechanism and biological function of UHRF1-DNMT1-mediated DNA methylation.
Ren Y. (2022)
9 other articles

1 mention without citation

Human PCNA Structure, Function and Interactions.
González-Magaña et al. (2020)