› 6fge

X-ray diffraction
1.74Å resolution

Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin

Released:
DOI: 10.2210/pdb6fge/pdb
PDB entry 6fge coloured by chain, front view.
PDB entry 6fge coloured by chain, side view.
PDB entry 6fge coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability.
Kwasna D, Abdul Rehman SA, Natarajan J, Matthews S, Madden R, De Cesare V, Weidlich S, Virdee S, Ahel I, Gibbs-Seymour I, Kulathu Y
Mol Cell 70 150-164.e6 (2018)
PMID: 29576527

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:
  • 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-143286 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Zinc finger-containing ubiquitin peptidase 1 Chain: A
Molecule details ›
Chain: A
Length: 348 amino acids
Theoretical weight: 39.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96AP4 (Residues: 231-578; Coverage: 60%)
Gene names: C6orf113, ZUFSP, ZUP1
Sequence domains: Peptidase family C78
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 76 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

7 bound ligands:
Ligand MLI 1 x MLI
Ligand EDO 3 x EDO
Ligand GOL 2 x GOL
Ligand FMT 7 x FMT
Ligand PEG 1 x PEG
Ligand NH4 2 x NH4
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6522
Unit cell:
a: 84.484Å b: 84.484Å c: 201.867Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.174 0.209
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

45 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
44 more

1 mention without citation

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability.
Kwasna et al. (2018)