2R7X

Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 

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:  

  • 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 an ...

    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase
A, B
1095Rotavirus A (strain RVA/SA11-Patton/G3P[X])Mutation(s): 0 
EC: 2.7.7.48
Find proteins for O37061 (Rotavirus A (strain RVA/SA11-Patton/G3P[X]))
Go to UniProtKB:  O37061
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')X,Y7N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.000α = 90.00
b = 143.766β = 90.65
c = 112.833γ = 90.00
Software Package:
Software NamePurpose
DMphasing
HKL-2000data scaling
SCALEPACKdata scaling
ADSCdata collection
HKL-2000data reduction
CNSphasing
DENZOdata reduction
SHARPphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description