The crystal structure of murine p97/VCP at 3.6A

Experimental Data Snapshot

  • Resolution: 3.60 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.327 
  • R-Value Observed: 0.327 

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This is version 1.4 of the entry. See complete history


The crystal structure of murine p97/VCP at 3.6A

Huyton, T.Pye, V.E.Briggs, L.C.Flynn, T.C.Beuron, F.Kondo, H.Ma, J.Zhang, X.Freemont, P.S.

(2003) J Struct Biol 144: 337-348

  • DOI: https://doi.org/10.1016/j.jsb.2003.10.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    p97/VCP is a member of the AAA ATPase family and has roles in both membrane fusion and ubiquitin dependent protein degradation. Here, we present a 3.6A crystal structure of murine p97 in which D2 domain has been modelled as poly-alanine and the remaining approximately 100 residues are absent. The resulting structure illustrates a head-to-tail packing arrangement of the two p97 AAA domains in a natural hexameric state with D1 ADP bound and D2 nucleotide free. The head-to-tail packing arrangement observed in this structure is in contrast to our previously predicted tail-to-tail packing model. The linker between the D1 and D2 domains is partially disordered, suggesting a flexible nature. Normal mode analysis of the crystal structure suggests anti-correlated motions and distinct conformational states of the two AAA domains.

  • Organizational Affiliation

    Department of Biological Sciences, Imperial College London, South Kensington SW7 2AZ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase816Mus musculusMutation(s): 0 
Gene Names: VCP
Find proteins for Q01853 (Mus musculus)
Explore Q01853 
Go to UniProtKB:  Q01853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01853
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.60 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.327 
  • R-Value Observed: 0.327 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.2α = 90
b = 145.2β = 90
c = 167.4γ = 120
Software Package:
Software NamePurpose
ProDCdata collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description