PDBe 5wvo

X-ray diffraction
2Å resolution

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:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: A, B
Molecule details ›
Chains: A, B
Length: 76 amino acids
Theoretical weight: 8.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpT4
UniProt:
  • Canonical: NEW P62979 (Residues: 1-76; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ubiquitin family
DNA (cytosine-5)-methyltransferase 1 Chain: C
Molecule details ›
Chain: C
Length: 250 amino acids
Theoretical weight: 27.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpT4
UniProt:
  • Canonical: NEW P26358 (Residues: 351-600; Coverage: 16%)
Gene names: AIM, CXXC9, DNMT, DNMT1
Sequence domains: Cytosine specific DNA methyltransferase replication foci domain
Histone H3.1 Chain: D
Molecule details ›
Chain: D
Length: 37 amino acids
Theoretical weight: 3.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpT4
UniProt:
  • Canonical: NEW P68431 (Residues: 2-37; Coverage: 27%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: C2221
Unit cell:
a: 68.362Å b: 198.779Å c: 76.904Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.239
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpT4