1NG0

The three-dimensional structure of Cocksfoot mottle virus at 2.7A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The three-dimensional structure of cocksfoot mottle virus at 2.7 A resolution.

Tars, K.Zeltins, A.Liljas, L.

(2003) Virology 310: 287-297


  • PubMed Abstract: 
  • Cocksfoot mottle virus is a plant virus that belongs to the genus Sobemovirus. The structure of the virus has been determined at 2.7 A resolution. The icosahedral capsid has T = 3 quasisymmetry and 180 copies of the coat protein. Except for a couple ...

    Cocksfoot mottle virus is a plant virus that belongs to the genus Sobemovirus. The structure of the virus has been determined at 2.7 A resolution. The icosahedral capsid has T = 3 quasisymmetry and 180 copies of the coat protein. Except for a couple of stacked bases, the viral RNA is not visible in the electron density map. The coat protein has a jelly-roll beta-sandwich fold and its conformation is very similar to that of other sobemoviruses and tobacco necrosis virus. The N-terminal arm of one of the three quasiequivalent subunits is partly ordered and follows the same path in the capsid as the arm in rice yellow mottle virus, another sobemovirus. In other sobemoviruses, the ordered arm follows a different path, but in both cases the arms from three subunits meet and form a similar structure at a threefold axis. A comparison of the structures and sequences of viruses in this family shows that the only conserved parts of the protein-protein interfaces are those that form binding sites for calcium ions. Still, the relative orientations and position of the subunits are maintained.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Box 596, S751 24 Uppsala, Sweden. kaspars@xray.bmc.uu.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
coat protein
A, B, C
253Cocksfoot mottle virusGene Names: ORF4
Find proteins for Q9E958 (Cocksfoot mottle virus)
Go to UniProtKB:  Q9E958
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 291.069α = 90.00
b = 537.250β = 90.00
c = 555.158γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
TFmodel building
TFphasing
RAVEmodel building
RAVEphasing
GLRFphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-12-20
    Type: Database references