3HU1

Structure of p97 N-D1 R95G mutant in complex with ATPgS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants.

Tang, W.K.Li, D.Li, C.C.Esser, L.Dai, R.Guo, L.Xia, D.

(2010) Embo J. 29: 2217-2229

  • DOI: 10.1038/emboj.2010.104
  • Primary Citation of Related Structures:  3HU2, 3HU3

  • PubMed Abstract: 
  • Mutations in p97, a major cytosolic AAA (ATPases associated with a variety of cellular activities) chaperone, cause inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). IBMPFD mutants have single a ...

    Mutations in p97, a major cytosolic AAA (ATPases associated with a variety of cellular activities) chaperone, cause inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). IBMPFD mutants have single amino-acid substitutions at the interface between the N-terminal domain (N-domain) and the adjacent AAA domain (D1), resulting in a reduced affinity for ADP. The structures of p97 N-D1 fragments bearing IBMPFD mutations adopt an atypical N-domain conformation in the presence of Mg(2+).ATPgammaS, which is reversible by ADP, showing for the first time the nucleotide-dependent conformational change of the N-domain. The transition from the ADP- to the ATPgammaS-bound state is accompanied by a loop-to-helix conversion in the N-D1 linker and by an apparent re-ordering in the N-terminal region of p97. X-ray scattering experiments suggest that wild-type p97 subunits undergo a similar nucleotide-dependent N-domain conformational change. We propose that IBMPFD mutations alter the timing of the transition between nucleotide states by destabilizing the ADP-bound form and consequently interfere with the interactions between the N-domains and their substrates.


    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, B, C, D, E, F
489Homo sapiensGene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Go to Gene View: VCP
Go to UniProtKB:  P55072
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ATGKd: 130 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.240 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 92.756α = 97.66
b = 103.279β = 91.88
c = 107.688γ = 89.75
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALEPACKdata scaling
REFMACrefinement
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-06-12 
  • Released Date: 2010-06-16 
  • Deposition Author(s): Tang, W.-K.

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-02-15
    Type: Non-polymer description