1SLQ

Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.308 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural rearrangements in the membrane penetration protein of a non-enveloped virus.

Dormitzer, P.R.Nason, E.B.Prasad, B.V.Harrison, S.C.

(2004) Nature 430: 1053-1058

  • DOI: 10.1038/nature02836

  • PubMed Abstract: 
  • Non-enveloped virus particles (those that lack a lipid-bilayer membrane) must breach the membrane of a target host cell to gain access to its cytoplasm. So far, the molecular mechanism of this membrane penetration step has resisted structural analysi ...

    Non-enveloped virus particles (those that lack a lipid-bilayer membrane) must breach the membrane of a target host cell to gain access to its cytoplasm. So far, the molecular mechanism of this membrane penetration step has resisted structural analysis. The spike protein VP4 is a principal component in the entry apparatus of rotavirus, a non-enveloped virus that causes gastroenteritis and kills 440,000 children each year. Trypsin cleavage of VP4 primes the virus for entry by triggering a rearrangement that rigidifies the VP4 spikes. We have determined the crystal structure, at 3.2 A resolution, of the main part of VP4 that projects from the virion. The crystal structure reveals a coiled-coil stabilized trimer. Comparison of this structure with the two-fold clustered VP4 spikes in a approximately 12 A resolution image reconstruction from electron cryomicroscopy of trypsin-primed virions shows that VP4 also undergoes a second rearrangement, in which the oligomer reorganizes and each subunit folds back on itself, translocating a potential membrane-interaction peptide from one end of the spike to the other. This rearrangement resembles the conformational transitions of membrane fusion proteins of enveloped viruses.


    Related Citations: 
    • The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site
      Dormitzer, P.R.,Sun, Z.-Y.J.,Wagner, G.,Harrison, S.C.
      (2002) Embo J. 21: 885
    • A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning
      Padilla, J.E.,Yeates, T.O.
      (2003) Acta Crystallogr.,Sect.D 59: 1124
    • Proteolysis of monomeric recombinant rotavirus VP4 yields an oligomeric VP5* core
      Dormitzer, P.R.,Greenberg, H.B.,Harrison, S.C.
      (2001) J.Virol. 75: 7339


    Organizational Affiliation

    Department of Pediatrics, Harvard Medical School, and the Laboratory of Molecular Medicine, Children's Hospital, Boston, Massachusetts 02115, USA. dormitze@crystal.harvard.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP4
A, B, C, D, E, F
278Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])Mutation(s): 0 
Find proteins for P12473 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Go to UniProtKB:  P12473
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.308 
  • Space Group: P 42 2 2
Unit Cell:
Length (Å)Angle (°)
a = 244.843α = 90.00
b = 244.843β = 90.00
c = 104.778γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
MLPHAREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance