1DDL

DESMODIUM YELLOW MOTTLE TYMOVIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution.

Larson, S.B.Day, J.Canady, M.A.Greenwood, A.McPherson, A.

(2000) J.Mol.Biol. 301: 625-642

  • DOI: 10.1006/jmbi.2000.3983

  • PubMed Abstract: 
  • Desmodium yellow mottle virus is a 28 nm diameter, T=3 icosahedral plant virus of the tymovirus group. Its structure has been solved to a resolution of 2.7 A using X-ray diffraction analysis based on molecular replacement and phase extension methods. ...

    Desmodium yellow mottle virus is a 28 nm diameter, T=3 icosahedral plant virus of the tymovirus group. Its structure has been solved to a resolution of 2.7 A using X-ray diffraction analysis based on molecular replacement and phase extension methods. The final R value was 0.151 (R(free)=0.159) for 134,454 independent reflections. The folding of the polypeptide backbone is nearly identical with that of turnip yellow mosaic virus, as is the arrangement of subunits in the virus capsid. However, a major difference in the disposition of the amino-terminal ends of the subunits was observed. In turnip yellow mosaic virus, those from the B and C subunits comprising the hexameric capsomeres formed an annulus about the interior of the capsomere, while the corresponding N termini of the pentameric capsomere A subunits were not visible at all in electron density maps. In Desmodium yellow mottle tymovirus, amino termini from the A and B subunits combine to form the annuli, thereby resulting in a much strengthened association between the two types of capsomeres and an, apparently, more stable capsid. The first 13 residues of the C subunit were invisible in electron density maps. Two ordered fragments of single-stranded RNA, seven and two nucleotides in length, were observed. The ordered water structure of the virus particle was delineated and required 95 solvent molecules per protein subunit.


    Organizational Affiliation

    Department of Biochemistry, University of California, Irvine, CA 92697-3900, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DESMODIUM YELLOW MOTTLE VIRUS
A, B, C
188Desmodium yellow mottle virusN/A
Find proteins for O89511 (Desmodium yellow mottle virus)
Go to UniProtKB:  O89511
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')D7N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*U)-3')E2N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.151 
  • Space Group: P 42 3 2
Unit Cell:
Length (Å)Angle (°)
a = 348.546α = 90.00
b = 348.546β = 90.00
c = 348.546γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance