Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 91.06 kDa 
• Atom Count: 4680 
• Modelled Residue Count: 683 
• Deposited Residue Count: 816 
• Unique protein chains: 1

1R7R

The crystal structure of murine p97/VCP at 3.6A

• DOI: 10.2210/pdb1R7R/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-22 Released: 2003-12-16 
• Deposition Author(s): Huyton, T., Pye, V.E., Briggs, L.C., Flynn, T.C., Beuron, F., Kondo, H., Ma, J., Zhang, X., Freemont, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.358 
• R-Value Work: 0.327 
• R-Value Observed: 0.327 

Literature

The crystal structure of murine p97/VCP at 3.6A

Huyton, T., Pye, V.E., Briggs, L.C., Flynn, T.C., Beuron, F., Kondo, H., Ma, J., Zhang, X., Freemont, P.S.

(2003) J Struct Biol 144: 337-348

• PubMed: 14643202 
• DOI: 10.1016/j.jsb.2003.10.007
• Primary Citation of Related Structures:  
  1R7R


• PubMed Abstract: 
  

p97/VCP is a member of the AAA ATPase family and has roles in both membrane fusion and ubiquitin dependent protein degradation. Here, we present a 3.6A crystal structure of murine p97 in which D2 domain has been modelled as poly-alanine and the remaining approximately 100 residues are absent. The resulting structure illustrates a head-to-tail packing arrangement of the two p97 AAA domains in a natural hexameric state with D1 ADP bound and D2 nucleotide free. The head-to-tail packing arrangement observed in this structure is in contrast to our previously predicted tail-to-tail packing model. The linker between the D1 and D2 domains is partially disordered, suggesting a flexible nature. Normal mode analysis of the crystal structure suggests anti-correlated motions and distinct conformational states of the two AAA domains.

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Organizational Affiliation: 

Department of Biological Sciences, Imperial College London, South Kensington SW7 2AZ, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A	816	Mus musculus	Mutation(s): 0  Gene Names: Vcp EC: 3.6.4.6
Find proteins for Q01853 (Mus musculus) Explore Q01853  Go to UniProtKB:  Q01853

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.358 
• R-Value Work: 0.327 
• R-Value Observed: 0.327 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.2	α = 90
b = 145.2	β = 90
c = 167.4	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ProDC	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-22 
• Released Date: 2003-12-16 
Deposition Author(s): Huyton, T., Pye, V.E., Briggs, L.C., Flynn, T.C., Beuron, F., Kondo, H., Ma, J., Zhang, X., Freemont, P.S.

Revision History  

• Version 1.0: 2003-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description