2IZW

Crystal structure of Ryegrass Mottle Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.294 
  • R-Value Observed: 0.294 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Three-Dimensional Structure of Ryegrass Mottle Virus at 2.9 A Resolution.

Plevka, P.Tars, K.Zeltins, A.Balke, I.Truve, E.Liljas, L.

(2007) Virology 369: 364

  • DOI: 10.1016/j.virol.2007.07.028
  • Primary Citation of Related Structures:  
    2IZW

  • PubMed Abstract: 
  • The crystal structure of the sobemovirus Ryegrass mottle virus (RGMoV) has been determined at 2.9 A resolution. The coat protein has a canonical jellyroll beta-sandwich fold. In comparison to other sobemoviruses the RGMoV coat protein is missing several residues in two of the loop regions ...

    The crystal structure of the sobemovirus Ryegrass mottle virus (RGMoV) has been determined at 2.9 A resolution. The coat protein has a canonical jellyroll beta-sandwich fold. In comparison to other sobemoviruses the RGMoV coat protein is missing several residues in two of the loop regions. The first loop contributes to contacts between subunits around the quasi-threefold symmetry axis. The altered contact interface results in tilting of the subunits towards the quasi-threefold axis. The assembly of the T=3 capsid of sobemoviruses is controlled by the N-termini of C subunits forming a so-called beta-annulus. The other loop that is smaller in the RGMoV structure contains a helix that participates in stabilization of the beta-annulus in other sobemoviruses. The loss of interaction between the RGMoV loop and the beta-annulus has been compensated for by additional interactions between the N-terminal arms. As a consequence of these differences, the diameter of the RGMoV particle is 8 A smaller than that of the other sobemoviruses. The interactions of coat proteins in sobemovirus capsids involve calcium ions. Depletion of calcium ions results in particle swelling, which is considered a first step in disassembly. We could not identify any density for metal ions in the proximity of the conserved residues normally involved in calcium binding, but the RGMoV structure does not show any signs of swelling. A likely reason is the low pH (3.0) of the crystallization buffer in which the groups interacting with the calcium ions are not charged.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RYEGRASS MOTTLE VIRUS COAT PROTEINA, B, C234Ryegrass mottle virusMutation(s): 0 
Gene Names: ORF4CP
UniProt
Find proteins for Q9E962 (Ryegrass mottle virus)
Explore Q9E962 
Go to UniProtKB:  Q9E962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9E962
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.294 
  • R-Value Observed: 0.294 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 277.641α = 90
b = 298.719β = 92.74
c = 392.485γ = 90
Software Package:
Software NamePurpose
CCP4Imodel building
SCALEPACKdata scaling
AVEphasing
CNSphasing
GLRFphasing
CCP4Iphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation