2R7O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-dependent RNA polymeraseA1095Simian rotavirusMutation(s): 0 
Gene Names: gene 1
EC: 2.7.7.48
UniProt
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
SHARPphasing
DMphasing
CNSrefinement
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