› 2zo0

X-ray diffraction
2.19Å resolution

mouse NP95 SRA domain DNA specific complex 1

Released:
DOI: 10.2210/pdb2zo0/pdb
PDB entry 2zo0 coloured by chain, front view.
PDB entry 2zo0 coloured by chain, side view.
PDB entry 2zo0 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X
Nature 455 826-9 (2008)
PMID: 18772888

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 domain:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
hetero dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-115971 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase UHRF1 Chain: B
Molecule details ›
Chain: 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
DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3') Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3') Chain: E
Molecule details ›
Chain: E
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 61.982Å b: 69.008Å c: 92.956Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.253
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

83 review citations

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law et al. (2010)
82 more

3 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
2 more