Crystal structure of the USP8 interaction domain of human NRDP1

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8).

Avvakumov, G.V.Walker, J.R.Xue, S.Finerty Jr., P.J.Mackenzie, F.Newman, E.M.Dhe-Paganon, S.

(2006) J Biol Chem 281: 38061-38070

  • DOI: https://doi.org/10.1074/jbc.M606704200
  • Primary Citation of Related Structures:  
    2A9U, 2FZP, 2GFO, 2GWF

  • PubMed Abstract: 

    Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil, rhodanese, and catalytic domains. We report the first high-resolution crystal structures of these domains and discuss their implications for USP8 function. The amino-terminal domain is a homodimer with a novel fold. It is composed of two five-helix bundles, where the first helices are swapped, and carboxyl-terminal helices are extended in an antiparallel fashion. The structure of the rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals the canonical rhodanese fold but with a distorted primordial active site. The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. A consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the carboxyl-terminal catalytic domain of USP8 exhibits the conserved tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes.

  • Organizational Affiliation

    Structural Genomics Consortium and the Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ring finger protein 41 isoform 1144Homo sapiensMutation(s): 0 
Gene Names: RNF41
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4P4 (Homo sapiens)
Explore Q9H4P4 
Go to UniProtKB:  Q9H4P4
GTEx:  ENSG00000181852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H4P4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.796α = 90
b = 44.262β = 90
c = 88.339γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
ARP/wARPmodel building

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references