› 8xqc

Electron Microscopy
3.25Å resolution

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog

Released:
DOI: 10.2210/pdb8xqc/pdb
PDB entry 8xqc coloured by chain, front view.
PDB entry 8xqc coloured by chain, side view.
PDB entry 8xqc coloured by chain, top view.
Source organisms:
Entry authors: Kikuchi A, Hayashi G, Kori S, Arita K
Related structures: EMD-38573

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-283782 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 1 Chain: A
Molecule details ›
Chain: A
Length: 1271 amino acids
Theoretical weight: 143.56 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P26358 (Residues: 351-1616; Coverage: 78%)
Gene names: AIM, CXXC9, DNMT, DNMT1
Sequence domains:
DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.73 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3') Chain: C

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand ZN 2 x ZN
2 modified residues:
Ligand 5CM 1 x 5CM
Ligand EIX 1 x EIX

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.25Å
Relevant EMDB volumes: EMD-38573
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links