Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 21208.71 
• Atom Count: 1363 
• Residue Count: 186 
• Unique protein chains: 1

3QQ7

Crystal Structure of the p97 N-terminal domain

• DOI: 10.2210/pdb3QQ7/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-02-15 Released: 2011-06-22 
• Deposition Author(s): Haenzelmann, P., Schindelin, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 

Literature

Hierarchical Binding of Cofactors to the AAA ATPase p97.

Hanzelmann, P., Buchberger, A., Schindelin, H.

(2011) Structure 19: 833-843

• PubMed: 21645854 
• DOI: 10.1016/j.str.2011.03.018
• Primary Citation of Related Structures:  
  3R3M, 3QQ8


• PubMed Abstract: 
  

The hexameric AAA ATPase p97 is involved in several human proteinopathies and mediates ubiquitin-dependent protein degradation among other essential cellular processes. Via its N-terminal domain (N domain), p97 interacts with multiple regulatory cofactors including the UFD1/NPL4 heterodimer and members of the "ubiquitin regulatory X" (UBX) domain protein family; however, the principles governing cofactor selectivity remain to be deciphered. Our crystal structure of the FAS-associated factor 1 (FAF1)UBX domain in complex with the p97N domain reveals that the signature Phe-Pro-Arg motif known to be crucial for interactions of UBX domains with p97 adopts a cis-proline configuration, in contrast to a cis-trans mixture we derive for the isolated FAF1UBX domain. Biochemical studies confirm that binding critically depends on a proline at this position. Furthermore, we observe that the UBX proteins FAF1 and UBXD7 only bind to p97-UFD1/NPL4, but not free p97, thus demonstrating for the first time a hierarchy in p97-cofactor interactions.

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Organizational Affiliation: 

Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transitional endoplasmic reticulum ATPase	A	186	Homo sapiens	Mutation(s): 0  Gene 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEZ	A	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO	A	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• Space Group: P 3₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.560	α = 90.00
b = 60.560	β = 90.00
c = 63.110	γ = 120.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-15 
• Released Date: 2011-06-22 
• Deposition Author(s): Haenzelmann, P., Schindelin, H.

Revision History 

• Version 1.0: 2011-06-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-08
  Type: Refinement description