1P3Q

Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p.

Prag, G.Misra, S.Jones, E.A.Ghirlando, R.Davies, B.A.Horazdovsky, B.F.Hurley, J.H.

(2003) Cell 113: 609-620

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coupling of ubiquitin conjugation to ER degradation (CUE) domains are approximately 50 amino acid monoubiquitin binding motifs found in proteins of trafficking and ubiquitination pathways. The 2.3 A structure of the Vps9p-CUE domain is a dimeric doma ...

    Coupling of ubiquitin conjugation to ER degradation (CUE) domains are approximately 50 amino acid monoubiquitin binding motifs found in proteins of trafficking and ubiquitination pathways. The 2.3 A structure of the Vps9p-CUE domain is a dimeric domain-swapped variant of the ubiquitin binding UBA domain. The 1.7 A structure of the CUE:ubiquitin complex shows that one CUE dimer binds one ubiquitin molecule. The bound CUE dimer is kinked relative to the unbound CUE dimer and wraps around ubiquitin. The CUE monomer contains two ubiquitin binding surfaces on opposite faces of the molecule that cannot bind simultaneously to a single ubiquitin molecule. Dimerization of the CUE domain allows both surfaces to contact a single ubiquitin molecule, providing a mechanism for high-affinity binding to monoubiquitin.


    Related Citations: 
    • A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain
      Shih, S.C.,Prag, G.,Francis, S.A.,Sutanto, M.A.,Hurley, J.H.,Hicke, L.
      (2003) Embo J. 22: 1273


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein VPS9
Q, R
54Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: VPS9 (VPT9)
Find proteins for P54787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54787
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
U, V
76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Go to Gene View: UBC
Go to UniProtKB:  P0CH28
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
Q, R
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.607α = 90.00
b = 45.887β = 96.53
c = 57.802γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
MAR345data collection
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description