3CF0

Structure of D2 subdomain of P97/VCP in complex with ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.

    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, E, F, G, H, I, J, K, L, M, N
301Mus musculusMutation(s): 0 
Gene Names: Vcp
EC: 3.6.4.6
Find proteins for Q01853 (Mus musculus)
Go to UniProtKB:  Q01853
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.317α = 90.00
b = 167.223β = 112.29
c = 209.465γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance