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: 536.56 kDa 
• Atom Count: 32773 
• Modelled Residue Count: 4191 
• Deposited Residue Count: 4830 
• Unique protein chains: 1

5C19

p97 variant 2 in the apo state

• PDB DOI: 10.2210/pdb5C19/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-06-13 Released: 2016-01-13 
• Deposition Author(s): Haenzelmann, P., Schindelin, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.302 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

Literature

Structural Basis of ATP Hydrolysis and Intersubunit Signaling in the AAA+ ATPase p97.

Hanzelmann, P., Schindelin, H.

(2016) Structure 24: 127-139

• PubMed: 26712278 
• DOI: 10.1016/j.str.2015.10.026
• Primary Citation of Related Structures:  
  5C18, 5C19, 5C1A


• PubMed Abstract: 
  

p97 belongs to the superfamily of AAA+ ATPases and is characterized by a tandem AAA module, an N-terminal domain involved in substrate and cofactor interactions, and a functionally important unstructured C-terminal tail. The ATPase activity is controlled by an intradomain communication within the same protomer and an interdomain communication between neighboring protomers. Here, we present for the first time crystal structures in which the physiologically relevant p97 hexamer constitutes the content of the asymmetric unit, namely in the apo state without nucleotide in either the D1 or D2 module and in the pre-activated state with ATPγS bound to both modules. The structures provide new mechanistic insights into the interdomain communication mediated by conformational changes of the C terminus as well as an intersubunit signaling network, which couples the nucleotide state to the conformation of the central putative substrate binding pore.

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Organizational Affiliation: 

Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	805	Homo sapiens	Mutation(s): 4  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.302 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.665	α = 90
b = 165.78	β = 90
c = 243.992	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
MxCuBE	data collection
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-13 
• Released Date: 2016-01-13 
Deposition Author(s): Haenzelmann, P., Schindelin, H.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references