2IS9 | pdb_00002is9

Structure of yeast DCN-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.240 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2IS9

This is version 1.4 of the entry. See complete history

Literature

Structural basis for the function of DCN-1 in protein Neddylation.

Yang, X.Zhou, J.Sun, L.Wei, Z.Gao, J.Gong, W.Xu, R.M.Rao, Z.Liu, Y.

(2007) J Biological Chem 282: 24490-24494

  • DOI: https://doi.org/10.1074/jbc.C700038200
  • Primary Citation Related Structures: 
    2IS9

  • PubMed Abstract: 

    Covalent modification by Nedd8 (neddylation) stimulates the ubiquitin-protein isopeptide ligase (E3) activities of Cullins. DCN-1, an evolutionarily conserved protein, promotes neddylation of Cullins in vivo, binds directly to Nedd8, and associates with Cdc53 in the budding yeast Saccharomyces cerevisiae. The 1.9A resolution structure of yeast DCN-1 shows that the region encompassing residues 66-269 has a rectangular parallelepiped-like all alpha-helical structures, consisting of an EF-hand motif N-terminal domain and a closely juxtaposed C-terminal domain with six alpha-helices. The EF-hand motif structure is highly similar to that of the c-Cbl ubiquitin E3 ligase. We also demonstrate that DCN-1 directly binds to Rbx-1, a factor important for protein neddylation. The structural and biochemical results are consistent with the role of DCN-1 as a scaffold protein in a multisubunit neddylation E3 ligase complex.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 25.15 kDa 
  • Atom Count: 1,924 
  • Modeled Residue Count: 204 
  • Deposited Residue Count: 204 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Defective in cullin neddylation protein 1204Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DCN1
UniProt
Find proteins for Q12395 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12395 
Go to UniProtKB:  Q12395
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12395
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.107α = 90
b = 81.107β = 90
c = 106.023γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations