7VCS

Human p97 double hexamer conformer II with ATPgammaS bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of human p97 double hexamer capture potentiated ATPase-competent state.

Gao, H.Li, F.Ji, Z.Shi, Z.Li, Y.Yu, H.

(2022) Cell Discov 8: 19-19

  • DOI: https://doi.org/10.1038/s41421-022-00379-1
  • Primary Citation of Related Structures:  
    7VCS, 7VCT, 7VCU, 7VCV, 7VCX

  • PubMed Abstract: 

    The conserved ATPase p97 (Cdc48 in yeast) and adaptors mediate diverse cellular processes through unfolding polyubiquitinated proteins and extracting them from macromolecular assemblies and membranes for disaggregation and degradation. The tandem ATPase domains (D1 and D2) of the p97/Cdc48 hexamer form stacked rings. p97/Cdc48 can unfold substrates by threading them through the central pore. The pore loops critical for substrate unfolding are, however, not well-ordered in substrate-free p97/Cdc48 conformations. How p97/Cdc48 organizes its pore loops for substrate engagement is unclear. Here we show that p97/Cdc48 can form double hexamers (DH) connected through the D2 ring. Cryo-EM structures of p97 DH reveal an ATPase-competent conformation with ordered pore loops. The C-terminal extension (CTE) links neighboring D2s in each hexamer and expands the central pore of the D2 ring. Mutations of Cdc48 CTE abolish substrate unfolding. We propose that the p97/Cdc48 DH captures a potentiated state poised for substrate engagement.


  • Organizational Affiliation

    School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. gaohaishan@westlake.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
812Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
DA [auth F]
EA [auth G]
GA [auth G]
AA [auth E],
BA [auth F],
DA [auth F],
EA [auth G],
GA [auth G],
HA [auth H],
JA [auth H],
KA [auth I],
M [auth A],
MA [auth I],
NA [auth J],
O [auth A],
P [auth B],
PA [auth J],
QA [auth K],
R [auth B],
S [auth C],
SA [auth K],
TA [auth L],
U [auth C],
V [auth D],
VA [auth L],
X [auth D],
Y [auth E]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth F]
FA [auth G]
IA [auth H]
LA [auth I]
N [auth A]
CA [auth F],
FA [auth G],
IA [auth H],
LA [auth I],
N [auth A],
OA [auth J],
Q [auth B],
RA [auth K],
T [auth C],
UA [auth L],
W [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesI-1441
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP160667-P2
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170644

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Refinement description