PDBe 5cvo

X-ray diffraction
3.88Å resolution

WDR48:USP46~ubiquitin ternary complex

Released:

Function and Biology Details

Reaction catalysed:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
WD repeat-containing protein 48 Chains: A, D
Molecule details ›
Chains: A, D
Length: 677 amino acids
Theoretical weight: 72.9 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8TAF3 (Residues: 1-562; Coverage: 83%)
Gene names: KIAA1449, UAF1, WDR48
Sequence domains: WD domain, G-beta repeat
Ubiquitin carboxyl-terminal hydrolase 46 Chains: B, E
Molecule details ›
Chains: B, E
Length: 358 amino acids
Theoretical weight: 41.96 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P62068 (Residues: 25-366; Coverage: 93%)
  • Best match: P62068-2 (Residues: 1-217)
Gene name: USP46
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 96 amino acids
Theoretical weight: 10.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2
Unit cell:
a: 211.342Å b: 103.764Å c: 190.954Å
α: 90° β: 119.03° γ: 90°
R-values:
R R work R free
0.225 0.222 0.275
Expression system: Trichoplusia ni