› 4gy5

X-ray diffraction
2.96Å resolution

Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3

Released:
DOI: 10.2210/pdb4gy5/pdb
PDB entry 4gy5 coloured by chain, front view.
PDB entry 4gy5 coloured by chain, side view.
PDB entry 4gy5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein.
Cheng J, Yang Y, Fang J, Xiao J, Zhu T, Chen F, Wang P, Li Z, Yang H, Xu Y
J Biol Chem 288 1329-39 (2013)
PMID: 23161542

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:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-160866 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase UHRF1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 241 amino acids
Theoretical weight: 27.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96T88 (Residues: 134-366; Coverage: 29%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains:
Structure domains:
Histone H3.3 Chains: E, F
Molecule details ›
Chains: E, F
Length: 17 amino acids
Theoretical weight: 1.86 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P84243 (Residues: 2-18; Coverage: 13%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

1 bound ligand:
Ligand ZN 7 x ZN
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P42212
Unit cell:
a: 145.94Å b: 145.94Å c: 125.903Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.255 0.288
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

24 review citations

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

8 mentions without citation

DNA methylation pathways and their crosstalk with histone methylation.
Du et al. (2015)
7 more