5C1B | pdb_00005c1b

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 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.str.2015.10.027
  • Primary Citation 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. 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. Electronic address: petra.haenzelmann@virchow.uni-wuerzburg.de.

Macromolecule Content 

  • Total Structure Weight: 532.94 kDa 
  • Atom Count: 34,659 
  • Modeled Residue Count: 4,365 
  • Deposited Residue Count: 4,752 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
A, B, C, D, E, F
785Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin fusion degradation protein 1 homologG [auth V],
H [auth U]
21Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92890 (Homo sapiens)
Explore Q92890 
Go to UniProtKB:  Q92890
PHAROS:  Q92890
GTEx:  ENSG00000070010 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92890
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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]
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
GOL

Query on GOL



Download:Ideal Coordinates CCD File
MA [auth F],
NA [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
GA [auth E]
LA [auth F]
M [auth A]
R [auth B]
S [auth C]
GA [auth E],
LA [auth F],
M [auth A],
R [auth B],
S [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
EA [auth E]
FA [auth E]
JA [auth F]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free:  0.240 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
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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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description