› 2fzp

X-ray diffraction
1.87Å resolution

Crystal structure of the USP8 interaction domain of human NRDP1

Released:
DOI: 10.2210/pdb2fzp/pdb
PDB entry 2fzp coloured by chain, front view.
PDB entry 2fzp coloured by chain, side view.
PDB entry 2fzp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8).
Avvakumov GV, Walker JR, Xue S, Finerty PJ, Mackenzie F, Newman EM, Dhe-Paganon S
J Biol Chem 281 38061-70 (2006)
PMID: 17035239

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:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190616 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase NRDP1 Chain: A
Molecule details ›
Chain: A
Length: 144 amino acids
Theoretical weight: 16.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9H4P4 (Residues: 193-317; Coverage: 39%)
Gene names: FLRF, NRDP1, RNF41, SBBI03
Sequence domains: USP8 interacting

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P212121
Unit cell:
a: 34.796Å b: 44.262Å c: 88.339Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.169 0.232
Expression system: Escherichia coli BL21

Quick links

Citations

37 review citations

Breaking the chains: structure and function of the deubiquitinases.
Komander et al. (2009)
36 more

2 mentions without citation

Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins.
Langenberg et al. (2020)
1 more