1R7R | pdb_00001r7r

The crystal structure of murine p97/VCP at 3.6A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.358 (Depositor) 
  • R-Value Work: 
    0.327 (Depositor) 
  • R-Value Observed: 
    0.327 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

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 Related Structures: 
    1R7R

  • 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.

Macromolecule Content 

  • Total Structure Weight: 91.06 kDa 
  • Atom Count: 4,680 
  • Modeled Residue Count: 683 
  • Deposited Residue Count: 816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase816Mus musculusMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.358 (Depositor) 
  • R-Value Work:  0.327 (Depositor) 
  • R-Value Observed: 0.327 (Depositor) 
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
CNSrefinement
ProDCdata collection
SCALEPACKdata scaling
AMoREphasing

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