› 8jwu

X-ray diffraction
3.58Å resolution

PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker

Released:
DOI: 10.2210/pdb8jwu/pdb
Model geometry
Fit model/data
PDB entry 8jwu coloured by chain, front view.
PDB entry 8jwu coloured by chain, side view.
PDB entry 8jwu coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for PHF7-mediated ubiquitination of histone H3.
Lee HS, Bang I, You J, Jeong TK, Kim CR, Hwang M, Kim JS, Baek SH, Song JJ, Choi HJ
OpenAccess logo Genes Dev (2023)
PMID: 37993255

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-237042 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase PHF7; Ubiquitin-conjugating enzyme E2 D2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 458 amino acids
Theoretical weight: 51.44 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q9DAG9 (Residues: 28-307; Coverage: 91%)
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, Phf7, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand ZN 23 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: C2
Unit cell:
a: 210.54Å b: 102.05Å c: 78.64Å
α: 90° β: 95.922° γ: 90°
R-values:
R R work R free
0.221 0.216 0.264
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Molecular basis for PHF7-mediated ubiquitination of histone H3.
Lee et al. (2023)