5KIY

p97 ND1-A232E in complex with VIMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/celldisc.2017.45
  • Primary Citation of Related Structures:  

  • 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 do ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transitional endoplasmic reticulum ATPase
A
468Homo sapiensMutation(s): 1 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Go to Gene View: VCP
Go to UniProtKB:  P55072
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Selenoprotein S
B
81Homo sapiensMutation(s): 0 
Gene Names: SELENOS (SELS, VIMP)
Find proteins for Q9BQE4 (Homo sapiens)
Go to Gene View: SELENOS
Go to UniProtKB:  Q9BQE4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.193 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 144.998α = 90.00
b = 144.998β = 90.00
c = 119.817γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-17 
  • Released Date: 2017-12-20 
  • Deposition Author(s): Tang, W.K., Xia, D.

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references