PDBe 5ydr

X-ray diffraction
2Å resolution

Structure of DNMT1 RFTS domain in complex with ubiquitin

Released:

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)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chains: A, D
Molecule details ›
Chains: A, D
Length: 75 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-225; Coverage: 32%)
Gene name: UBB
DNA (cytosine-5)-methyltransferase 1 Chain: B
Molecule details ›
Chain: B
Length: 250 amino acids
Theoretical weight: 27.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P26358 (Residues: 351-599; Coverage: 15%)
Gene names: AIM, CXXC9, DNMT, DNMT1
Sequence domains: Cytosine specific DNA methyltransferase replication foci domain

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P65
Unit cell:
a: 131.76Å b: 131.76Å c: 61.025Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.198 0.232
Expression system: Escherichia coli