5VCA

VCP like ATPase from T. acidophilum (VAT)-Substrate bound conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of a AAA+ unfoldase in the process of unfolding substrate.

Ripstein, Z.A.Huang, R.Augustyniak, R.Kay, L.E.Rubinstein, J.L.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.25754
  • Primary Citation of Related Structures:  
    5VC7, 5VCA

  • PubMed Abstract: 

    AAA+ unfoldases are thought to unfold substrate through the central pore of their hexameric structures, but how this process occurs is not known. VAT, the Thermoplasma acidophilum homologue of eukaryotic CDC48/p97, works in conjunction with the proteasome to degrade misfolded or damaged proteins. We show that in the presence of ATP, VAT with its regulatory N-terminal domains removed unfolds other VAT complexes as substrate. We captured images of this transient process by electron cryomicroscopy (cryo-EM) to reveal the structure of the substrate-bound intermediate. Substrate binding breaks the six-fold symmetry of the complex, allowing five of the six VAT subunits to constrict into a tight helix that grips an ~80 Å stretch of unfolded protein. The structure suggests a processive hand-over-hand unfolding mechanism, where each VAT subunit releases the substrate in turn before re-engaging further along the target protein, thereby unfolding it.


  • Organizational Affiliation

    The Hospital for Sick Children Research Institute, Toronto, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VCP-like ATPase564Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: vatTa0840
UniProt
Find proteins for O05209 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore O05209 
Go to UniProtKB:  O05209
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05209
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC0.2
MODEL REFINEMENTPHENIX1.10.1-2155

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-81294
Canadian Institutes of Health Research (CIHR)CanadaMOP-133408

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Data collection
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2020-01-15
    Changes: Author supporting evidence