Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.22 kDa 
• Atom Count: 7392 
• Modelled Residue Count: 900 
• Deposited Residue Count: 978 
• Unique protein chains: 1

4KO8

Structure of p97 N-D1 R155H mutant in complex with ATPgS

• PDB DOI: 10.2210/pdb4KO8/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-11 Released: 2013-11-13 
• Deposition Author(s): Xia, D., Tang, W.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.205 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Altered Intersubunit Communication Is the Molecular Basis for Functional Defects of Pathogenic p97 Mutants.

Tang, W.K., Xia, D.

(2013) J Biol Chem 288: 36624-36635

• PubMed: 24196964 
• DOI: 10.1074/jbc.M113.488924
• Primary Citation of Related Structures:  
  4KLN, 4KO8, 4KOD


• PubMed Abstract: 
  

The human AAA ATPase p97 is a molecular chaperone essential in cellular proteostasis. Single amino acid substitutions in p97 have been linked to a clinical multiple-disorder condition known as inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia. How the mutations affect the molecular mechanism that governs the function of p97 remains unclear. Here, we show that within the hexameric ring of a mutant p97, D1 domains fail to regulate their respective nucleotide-binding states, as evidenced by the lower amount of prebound ADP, weaker ADP binding affinity, full occupancy of adenosine-5'-O-(3-thiotriphosphate) binding, and elevated overall ATPase activity, indicating a loss of communication among subunits. Defective communication between subunits is further illustrated by altered conformation in the side chain of residue Phe-360 that probes into the nucleotide-binding pocket from a neighboring subunit. Consequently, conformations of N domains in a hexameric ring of a mutant p97 become uncoordinated, thus impacting its ability to process substrate.

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Organizational Affiliation: 

From the Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A, B	489	Homo sapiens	Mutation(s): 1  Gene Names: p97, 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	C [auth A], E [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AGS	PDBBind:  4KO8	Kd: 70 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.205 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.206	α = 90
b = 134.206	β = 90
c = 182.886	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-11 
• Released Date: 2013-11-13 
Deposition Author(s): Xia, D., Tang, W.K.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2014-01-08
  Changes: Database references