3CF2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 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
  • Primary Citation of Related Structures:  

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


    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 ATPase
A, B, C, D
806Mus musculusMutation(s): 0 
Gene Names: Vcp
EC: 3.6.4.6
Find proteins for Q01853 (Mus musculus)
Go to UniProtKB:  Q01853
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.271 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 144.900α = 90.00
b = 144.900β = 90.00
c = 164.400γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSphasing
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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