2gwf

X-ray diffraction
2.3Å resolution

Structure of a USP8-NRDP1 complex

Released:

Function and Biology Details

Reactions 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).
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:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 8 Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 157 amino acids
Theoretical weight: 17.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P40818 (Residues: 181-318; Coverage: 12%)
Gene names: KIAA0055, UBPY, USP8
Sequence domains: Rhodanese-like domain
Structure domains: Rhodanese-like domain
E3 ubiquitin-protein ligase NRDP1 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 134 amino acids
Theoretical weight: 14.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9H4P4 (Residues: 193-317; Coverage: 39%)
Gene names: FLRF, NRDP1, RNF41, SBBI03

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P21
Unit cell:
a: 76.111Å b: 67.094Å c: 99.275Å
α: 90° β: 91.12° γ: 90°
R-values:
R R work R free
0.208 0.206 0.237
Expression system: Escherichia coli BL21