› 3fde

X-ray diffraction
1.41Å resolution

Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution

Released:
DOI: 10.2210/pdb3fde/pdb
PDB entry 3fde coloured by chain, front view.
PDB entry 3fde coloured by chain, side view.
PDB entry 3fde 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-116245 (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: 419-628; Coverage: 27%)
Gene names: Np95, Uhrf1
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Mus musculus
Expression system: Not provided
5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3' Chains: E, F
Molecule details ›
Chains: E, F
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand EDO 22 x EDO
Ligand NA 4 x NA
Ligand UNL 9 x UNL
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2221
Unit cell:
a: 84.678Å b: 103.691Å c: 149.838Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.151 0.149 0.186
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

28 review citations

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

13 mentions without citation

The other face of restriction: modification-dependent enzymes.
Loenen et al. (2014)
12 more