2VAK

Crystal structure of the avian reovirus inner capsid protein sigmaA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Avian Reovirus Inner Capsid Protein Sigmaa.

Guardado-Calvo, P.Vazquez-Iglesias, L.Martinez-Costas, J.Llamas-Saiz, A.L.Schoehn, G.Fox, G.C.Hermo-Parrado, X.L.Benavente, J.van Raaij, M.J.

(2008) J.Virol. 82: 11208

  • DOI: 10.1128/JVI.00733-08

  • PubMed Abstract: 
  • Avian reovirus, an important avian pathogen, expresses eight structural and four nonstructural proteins. The structural sigmaA protein is a major component of the inner capsid, clamping together lambdaA building blocks. sigmaA has also been implicate ...

    Avian reovirus, an important avian pathogen, expresses eight structural and four nonstructural proteins. The structural sigmaA protein is a major component of the inner capsid, clamping together lambdaA building blocks. sigmaA has also been implicated in the resistance of avian reovirus to the antiviral action of interferon by strongly binding double-stranded RNA in the host cell cytoplasm and thus inhibiting activation of the double-stranded RNA-dependent protein kinase. We have solved the structure of bacterially expressed sigmaA by molecular replacement and refined it using data to 2.3-A resolution. Twelve sigmaA molecules are present in the P1 unit cell, arranged as two short double helical hexamers. A positively charged patch is apparent on the surface of sigmaA on the inside of this helix and mutation of either of two key arginine residues (Arg155 and Arg273) within this patch abolishes double-stranded RNA binding. The structural data, together with gel shift assay, electron microscopy, and sedimentation velocity centrifugation results, provide evidence for cooperative binding of sigmaA to double-stranded RNA. The minimal length of double-stranded RNA required for sigmaA binding was observed to be 14 to 18 bp.


    Related Citations: 
    • Crystallization of the Avian Reovirus Double-Stranded RNA-Binding and Core Protein Sigmaa
      Hermo-Parrado, X.L.,Guardado-Calvo, P.,Llamas-Saiz, A.L.,Fox, G.C.,Vazquez-Iglesias, L.,Martinez-Costas, J.,Benavente, J.,van Raaij, M.J.
      (2007) Acta Crystallogr.,Sect.F 63: 426


    Organizational Affiliation

    Departamento de Bioquímica e Bioloxía Molecular, Facultade de Farmacia, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIGMA A
A, B, C, D, E, F, G, H, I, J, K, L
423Avian orthoreovirusMutation(s): 0 
Find proteins for Q9E6F8 (Avian orthoreovirus)
Go to UniProtKB:  Q9E6F8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.210 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 103.210α = 93.81
b = 129.909β = 105.05
c = 144.037γ = 98.16
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-14
    Type: Database references, Source and taxonomy