5C1B

p97-delta709-728 in complex with a UFD1-SHP peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions.

Hanzelmann, P., Schindelin, H.

(2016) Structure 24: 140-147

  • DOI: 10.1016/j.str.2015.10.027
  • Primary Citation of Related Structures:  
    5C1B

  • PubMed Abstract: 

    • The type II AAA ATPase p97 interacts with a large number of cofactors that regulate its function by recruiting it to different cellular pathways. Most of the cofactors interact with the N-terminal (N) domain of p97, either via ubiquitin-like domains or short linear binding motifs ...

    The type II AAA ATPase p97 interacts with a large number of cofactors that regulate its function by recruiting it to different cellular pathways. Most of the cofactors interact with the N-terminal (N) domain of p97, either via ubiquitin-like domains or short linear binding motifs. While some linear binding motifs form α helices, another group features short stretches of unstructured hydrophobic sequences as found in the so-called SHP (BS1, binding segment 1) motif. Here we present the crystal structure of a SHP-binding motif in complex with p97, which reveals a so far uncharacterized binding site on the p97 N domain that is different from the conserved binding surface of all other known p97 cofactors. This finding explains how cofactors like UFD1/NPL4 and p47 can utilize a bipartite binding mechanism to interact simultaneously with the same p97 monomer via their ubiquitin-like domain and SHP motif.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPaseA, B, C, D, E, F785Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
NIH Common Fund Data Resources
PHAROS:  P55072
GTEx:  ENSG00000165280
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin fusion degradation protein 1 homologH [auth U], G [auth V]21Homo sapiensMutation(s): 0 
Gene Names: UFD1, UFD1L
Find proteins for Q92890 (Homo sapiens)
Explore Q92890 
Go to UniProtKB:  Q92890
NIH Common Fund Data Resources
PHAROS:  Q92890
GTEx:  ENSG00000070010
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS
Download Ideal Coordinates CCD File 
CA [auth E] , DA [auth E] , HA [auth F] , I [auth A] , IA [auth F] , J [auth A] , N [auth B] , O [auth B] , 
CA [auth E],  DA [auth E],  HA [auth F],  I [auth A],  IA [auth F],  J [auth A],  N [auth B],  O [auth B],  T [auth C],  U [auth C],  Y [auth D],  Z [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 MA [auth F], NA [auth F]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
 GA [auth E], LA [auth F], M [auth A], R [auth B], S [auth C], X [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , EA [auth E] , FA [auth E] , JA [auth F] , K [auth A] , KA [auth F] , L [auth A] , 
AA [auth D],  BA [auth D],  EA [auth E],  FA [auth E],  JA [auth F],  K [auth A],  KA [auth F],  L [auth A],  P [auth B],  Q [auth B],  V [auth C],  W [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.715α = 90
b = 180.664β = 90
c = 254.958γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MxCuBEdata collection
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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