› 3sou

X-ray diffraction
1.8Å resolution

Structure of UHRF1 PHD finger in complex with histone H3 1-9 peptide

Released:
DOI: 10.2210/pdb3sou/pdb
PDB entry 3sou coloured by chain, front view.
PDB entry 3sou coloured by chain, side view.
PDB entry 3sou coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression.
Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y
Mol Cell 43 275-284 (2011)
PMID: 21777816

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

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-159437 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase UHRF1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 70 amino acids
Theoretical weight: 7.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96T88 (Residues: 298-367; Coverage: 9%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chains: D, E
Molecule details ›
Chains: D, E
Length: 9 amino acids
Theoretical weight: 1.06 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-10; Coverage: 7%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43212
Unit cell:
a: 43.218Å b: 43.218Å c: 184.347Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.216 0.243
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

44 review citations

Histone methylation: a dynamic mark in health, disease and inheritance.
Greer et al. (2012)
43 more

8 mentions without citation

Readout of epigenetic modifications.
Patel et al. (2013)
7 more