› 3db3

X-ray diffraction
2.4Å resolution

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide

Released:
DOI: 10.2210/pdb3db3/pdb
PDB entry 3db3 coloured by chain, front view.
PDB entry 3db3 coloured by chain, side view.
PDB entry 3db3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.
Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chédin F, Arrowsmith CH, Dhe-Paganon S
J Biol Chem 286 24300-11 (2011)
PMID: 21489993

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180740 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase UHRF1 Chain: A
Molecule details ›
Chain: A
Length: 161 amino acids
Theoretical weight: 19.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96T88 (Residues: 126-285; Coverage: 20%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains: Tandem tudor domain within UHRF1
Structure domains:
Histone H3.2 Chain: B
Molecule details ›
Chain: B
Length: 6 amino acids
Theoretical weight: 707 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 7-12; Coverage: 4%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D

Ligands and Environments

No bound ligands
2 modified residues:
Ligand MSE 4 x MSE
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P62
Unit cell:
a: 99.622Å b: 99.622Å c: 41.232Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.212 0.282
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

44 review citations

Modification of enhancer chromatin: what, how, and why?
Calo et al. (2013)
43 more

14 mentions without citation

Keeping it in the family: diverse histone recognition by conserved structural folds.
Yap et al. (2010)
13 more