3CF2

Structure of P97/vcp in complex with ADP/AMP-PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.

Davies, J.M.Brunger, A.T.Weis, W.I.

(2008) Structure 16: 715-726

  • DOI: 10.1016/j.str.2008.02.010
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The ATPases associated with various cellular activities (AAA) protein p97 has been implicated in a variety of cellular processes, including endoplasmic reticulum-associated degradation and homotypic membrane fusion. p97 belongs to a subgroup of AAA p ...

    The ATPases associated with various cellular activities (AAA) protein p97 has been implicated in a variety of cellular processes, including endoplasmic reticulum-associated degradation and homotypic membrane fusion. p97 belongs to a subgroup of AAA proteins that contains two nucleotide binding domains, D1 and D2. We determined the crystal structure of D2 at 3.0 A resolution. This model enabled rerefinement of full-length p97 in different nucleotide states against previously reported low-resolution diffraction data to significantly improved R values and Ramachandran statistics. Although the overall fold remained similar, there are significant improvements, especially around the D2 nucleotide binding site. The rerefinement illustrates the importance of knowledge of high-resolution structures of fragments covering most of the whole molecule. The structures suggest that nucleotide hydrolysis is transformed into larger conformational changes by pushing of one D2 domain by its neighbor in the hexamer, and transmission of nucleotide-state information through the D1-D2 linker to displace the N-terminal, effector binding domain.


    Related Citations: 
    • Complete Structure of P97/Valosin-Containing Protein Reveals Communication between Nucleotide Domains
      DelaBarre, B., Brunger, A.T.
      (2003) Nat Struct Mol Biol 10: 856
    • Nucleotide Dependent Motion and Mechanism of Action of P97/Vcp
      DelaBarre, B., Brunger, A.T.
      (2005) J Mol Biol 347: 437

    Organizational Affiliation

    Department of Structural Biology, Stanford University, Stanford, CA 94305-5432, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transitional endoplasmic reticulum ATPaseA, B, C, D806Mus musculusMutation(s): 0 
Gene Names: Vcp
EC: 3.6.4.6
Find proteins for Q01853 (Mus musculus)
Explore Q01853 
Go to UniProtKB:  Q01853
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.9α = 90
b = 144.9β = 90
c = 164.4γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-07
    Changes: Other