1DDL

DESMODIUM YELLOW MOTTLE TYMOVIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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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
  • Primary Citation of Related Structures:  
    1DDL

  • 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. The final R value was 0 ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DESMODIUM YELLOW MOTTLE VIRUSC [auth A],
D [auth B],
E [auth C]
188Desmodium yellow mottle virusMutation(s): 0 
UniProt
Find proteins for O89511 (Desmodium yellow mottle virus)
Explore O89511 
Go to UniProtKB:  O89511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO89511
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')A [auth D]7N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*U)-3')B [auth E]2N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 348.546α = 90
b = 348.546β = 90
c = 348.546γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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