Crystal Structure of VPS4B

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history


Structural and mechanistic studies of VPS4 proteins

Scott, A.Chung, H.Y.Gonciarz-Swiatek, M.Hill, G.C.Whitby, F.G.Gaspar, J.Holton, J.M.Viswanathan, R.Ghaffarian, S.Hill, C.P.Sundquist, W.I.

(2005) EMBO J 24: 3658-3669

  • DOI: https://doi.org/10.1038/sj.emboj.7600818
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    VPS4 ATPases function in multivesicular body formation and in HIV-1 budding. Here, we report the crystal structure of monomeric apo human VPS4B/SKD1 (hVPS4B), which is composed of five distinct elements: a poorly ordered N-terminal MIT domain that binds ESCRT-III substrates, large (mixed alpha/beta) and small (alpha) AAA ATPase domains that closely resemble analogous domains in the p97 D1 ATPase cassette, a three-stranded antiparallel beta domain inserted within the small ATPase domain, and a novel C-terminal helix. Apo hVPS4B and yeast Vps4p (yVps4p) proteins dimerized in solution, and assembled into larger complexes (10-12 subunits) upon ATP binding. Human and yeast adaptor proteins (LIP5 and yVta1p, respectively) bound the beta domains of the fully assembled hVPS4B and yVps4p proteins. We therefore propose that Vps4 proteins cycle between soluble, inactive low molecular weight complexes and active, membrane-associated double-ring structures that bind ATP and coassemble with LIP5/Vta1. Finally, HIV-1 budding was inhibited by mutations in a loop that projects into the center of the modeled hVPS4B rings, suggesting that hVPS4B may release the assembled ESCRT machinery by pulling ESCRT-III substrates up into the central pore.

  • Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT 84132-3201, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SKD1 protein322Homo sapiensMutation(s): 0 
Gene Names: VPS4BSKD1VPS42
UniProt & NIH Common Fund Data Resources
Find proteins for O75351 (Homo sapiens)
Explore O75351 
Go to UniProtKB:  O75351
GTEx:  ENSG00000119541 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75351
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.199 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.058α = 90
b = 88.058β = 90
c = 112.574γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations