Crystal Structure of VP1 apoenzyme of Rotavirus SA11 (N-terminal hexahistidine-tagged)

Experimental Data Snapshot

  • Resolution: 3.35 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.235 

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Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.

Lu, X.McDonald, S.M.Tortorici, M.A.Tao, Y.J.Vasquez-Del Carpio, R.Nibert, M.L.Patton, J.T.Harrison, S.C.

(2008) Structure 16: 1678-1688

  • DOI: https://doi.org/10.1016/j.str.2008.09.006
  • Primary Citation of Related Structures:  
    2R7O, 2R7Q, 2R7R, 2R7S, 2R7T, 2R7U, 2R7V, 2R7W, 2R7X

  • PubMed Abstract: 

    Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 A resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus lambda3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.

  • Organizational Affiliation

    Laboratory of Molecular Medicine, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase1,095Simian rotavirusMutation(s): 0 
Gene Names: gene 1
Find proteins for O37061 (Rotavirus A (strain RVA/SA11-Patton/G3P[X]))
Explore O37061 
Go to UniProtKB:  O37061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO37061
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.35 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.903α = 90
b = 112.078β = 90
c = 142.814γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references