1XT9

Crystal Structure of Den1 in complex with Nedd8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a Complex between Nedd8 and the Ulp/Senp Protease Family Member Den1.

Reverter, D.Wu, K.Erdene, T.G.Pan, Z.Q.Wilkinson, K.D.Lima, C.D.

(2005) J Mol Biol 345: 141-151

  • DOI: https://doi.org/10.1016/j.jmb.2004.10.022
  • Primary Citation of Related Structures:  
    1XT9

  • PubMed Abstract: 

    The Nedd8 conjugation pathway is conserved from yeast to humans and is essential in many organisms. Nedd8 is conjugated to cullin proteins in a process that alters SCF E3 ubiquitin ligase activity, and it is presumed that Nedd8 deconjugation would reverse these effects. We now report the X-ray structures of the human Nedd8-specific protease, Den1, in a complex with the inhibitor Nedd8 aldehyde, thus revealing a model for the tetrahedral transition state intermediate generated during proteolysis. Although Den1 is closely related to the SUMO-specific protease family (Ulp/Senp family), structural analysis of the interface suggests determinants involved in Nedd8 selectivity by Den1 over other ubiquitin-like family members and suggests how the Ulp/Senp architecture has been modified to interact with different ubiquitin-like modifiers.


  • Organizational Affiliation

    Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sentrin-specific protease 8212Homo sapiensMutation(s): 0 
Gene Names: SENP8FKSG8PRSC2
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LD8 (Homo sapiens)
Explore Q96LD8 
Go to UniProtKB:  Q96LD8
PHAROS:  Q96LD8
GTEx:  ENSG00000166192 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LD8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neddylin76Homo sapiensMutation(s): 0 
Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
PHAROS:  Q15843
GTEx:  ENSG00000129559 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15843
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.849α = 90
b = 71.626β = 90
c = 52.947γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary