3R3M

Crystal structure of the FAF1 UBX domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hierarchical Binding of Cofactors to the AAA ATPase p97.

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

(2011) Structure 19: 833-843

  • DOI: 10.1016/j.str.2011.03.018
  • Primary Citation of Related Structures:  
    3QQ7, 3QQ8, 3R3M

  • 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 cofa ...

    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.


    Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany. petra.haenzelmann@virchow.uni-wuerzburg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAS-associated factor 1ABCD85Homo sapiensMutation(s): 0 
Gene Names: FAF1UBXD12UBXN3ACGI-03
Find proteins for Q9UNN5 (Homo sapiens)
Explore Q9UNN5 
Go to UniProtKB:  Q9UNN5
NIH Common Fund Data Resources
PHAROS  Q9UNN5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.755α = 90
b = 92.755β = 90
c = 108.5γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description