4LCB | pdb_00004lcb

Structure of Vps4 homolog from Acidianus hospitalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.254 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The Oligomeric State of the Active Vps4 AAA ATPase.

Monroe, N.Han, H.Gonciarz, M.D.Eckert, D.M.Karren, M.A.Whitby, F.G.Sundquist, W.I.Hill, C.P.

(2014) J Mol Biology 426: 510-525

  • DOI: https://doi.org/10.1016/j.jmb.2013.09.043
  • Primary Citation Related Structures: 
    4LCB, 4LGM

  • PubMed Abstract: 

    The cellular ESCRT (endosomal sorting complexes required for transport) pathway drives membrane constriction toward the cytosol and effects membrane fission during cytokinesis, endosomal sorting, and the release of many enveloped viruses, including the human immunodeficiency virus. A component of this pathway, the AAA ATPase Vps4, provides energy for pathway progression. Although it is established that Vps4 functions as an oligomer, subunit stoichiometry and other fundamental features of the functional enzyme are unclear. Here, we report that although some mutant Vps4 proteins form dodecameric assemblies, active wild-type Saccharomyces cerevisiae and Sulfolobus solfataricus Vps4 enzymes can form hexamers in the presence of ATP and ADP, as assayed by size-exclusion chromatography and equilibrium analytical ultracentrifugation. The Vta1p activator binds hexameric yeast Vps4p without changing the oligomeric state of Vps4p, implying that the active Vta1p-Vps4p complex also contains a single hexameric ring. Additionally, we report crystal structures of two different archaeal Vps4 homologs, whose structures and lattice interactions suggest a conserved mode of oligomerization. Disruption of the proposed hexamerization interface by mutagenesis abolished the ATPase activity of archaeal Vps4 proteins and blocked Vps4p function in S. cerevisiae. These data challenge the prevailing model that active Vps4 is a double-ring dodecamer, and argue that, like other type I AAA ATPases, Vps4 functions as a single ring with six subunits.


  • Organizational Affiliation
    • Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East RM 4100, Salt Lake City, UT 84112-5650, USA.

Macromolecule Content 

  • Total Structure Weight: 42.29 kDa 
  • Atom Count: 2,142 
  • Modeled Residue Count: 252 
  • Deposited Residue Count: 367 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division protein CdvC, Vps4367Acidianus hospitalis W1Mutation(s): 0 
UniProt
Find proteins for F4B4B0 (Acidianus hospitalis (strain W1))
Explore F4B4B0 
Go to UniProtKB:  F4B4B0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4B4B0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.254 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.962α = 90
b = 95.962β = 90
c = 79.499γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description