5KIW

p97 ND1-L198W in complex with VIMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for nucleotide-modulated p97 association with the ER membrane.

Tang, W.K.Zhang, T.Ye, Y.Xia, D.

(2017) Cell Discov 3: 17045-17045

  • DOI: https://doi.org/10.1038/celldisc.2017.45
  • Primary Citation of Related Structures:  
    5KIU, 5KIW, 5KIY

  • PubMed Abstract: 

    Association of the cytosolic AAA (ATPases associated with various cellular activities) protein p97 to membranes is essential for various cellular processes including endoplasmic reticulum (ER)-associated degradation. The p97 consists of two ATPase domains and an N domain that interacts with numerous cofactors. The N domain of p97 is known to undergo a large nucleotide-dependent conformation switch, but its physiological relevance is unclear. Here we show p97 is recruited to canine ER membranes predominantly by interacting with VCP-interacting membrane protein (VIMP), an ER-resident protein. We found that the recruitment is modulated through a nucleotide-dependent conformation switch of the N domain in wild-type p97, but this modulation is absent in pathogenic mutants. We demonstrate the molecular mechanism of the modulation by a series of structures of p97, VIMP and their complexes and suggest a physiological role of the nucleotide-dependent N domain conformation switch. The lack of modulation in pathogenic mutants is caused by changes in interactions between the N and D1 domain, as demonstrated by multiple intermediate positions adopted by N domains of mutant p97. Our findings suggest the nucleotide-modulated membrane association may also have a role in other p97-dependent processes.


  • Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B
468Homo sapiensMutation(s): 1 
Gene Names: VCP
EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
PHAROS:  P55072
GTEx:  ENSG00000165280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Selenoprotein S
C, D
81Homo sapiensMutation(s): 0 
Gene Names: VIMPSELSAD-015SBBI8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQE4 (Homo sapiens)
Explore Q9BQE4 
Go to UniProtKB:  Q9BQE4
PHAROS:  Q9BQE4
GTEx:  ENSG00000131871 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQE4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.772α = 90
b = 153.772β = 90
c = 240.641γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description