› 4pw5

X-ray diffraction
2.2Å resolution

structure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex I

Released:
DOI: 10.2210/pdb4pw5/pdb
PDB entry 4pw5 coloured by chain, front view.
PDB entry 4pw5 coloured by chain, side view.
PDB entry 4pw5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for hydroxymethylcytosine recognition by the SRA domain of UHRF2.
Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu RM
Mol Cell 54 879-86 (2014)
PMID: 24813944

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117988 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase UHRF2 Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 230 amino acids
Theoretical weight: 25.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96PU4 (Residues: 419-648; Coverage: 29%)
Gene names: NIRF, RNF107, UHRF2
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
5hmC-containing DNA1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 12 nucleotides
Theoretical weight: 3.72 KDa
Source organism: Homo sapiens
Expression system: Not provided
5hmC-containing DNA2 Chains: D, H
Molecule details ›
Chains: D, H
Length: 12 nucleotides
Theoretical weight: 3.59 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 42.273Å b: 82.807Å c: 82.864Å
α: 90.05° β: 90° γ: 89.98°
R-values:
R R work R free
0.163 0.161 0.206
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

24 review citations

Role of TET enzymes in DNA methylation, development, and cancer.
Rasmussen et al. (2016)
23 more

5 mentions without citation

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