› 3f8i

X-ray diffraction
2.29Å resolution

Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21

Released:
DOI: 10.2210/pdb3f8i/pdb
PDB entry 3f8i coloured by chain, front view.
PDB entry 3f8i coloured by chain, side view.
PDB entry 3f8i coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
Hashimoto H, Horton JR, Zhang X, Cheng X
Epigenetics 4 8-14 (2009)
PMID: 19077538

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116239 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase UHRF1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 212 amino acids
Theoretical weight: 23.92 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8VDF2 (Residues: 418-628; Coverage: 27%)
Gene names: Np95, Uhrf1
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Mus musculus
Expression system: Not provided
5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3' Chains: E, G
Molecule details ›
Chains: E, G
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 50.084Å b: 62.416Å c: 113.447Å
α: 90° β: 98.92° γ: 90°
R-values:
R R work R free
0.223 0.223 0.268
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

28 review citations

DNA methylation and its basic function.
Moore et al. (2013)
27 more

2 mentions without citation

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
Hashimoto et al. (2009)
1 more