Structure of Turnip Yellow Mosaic Virus at 100 K

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 

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The RNA of turnip yellow mosaic virus exhibits icosahedral order.

Larson, S.B.Lucas, R.W.Greenwood, A.McPherson, A.

(2005) Virology 334: 245-254

  • DOI: https://doi.org/10.1016/j.virol.2005.01.036
  • Primary Citation of Related Structures:  
    2FZ1, 2FZ2

  • PubMed Abstract: 

    Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded loops of RNA invade the pentameric and hexameric capsomeres where they contact the interior capsid surface. The remaining RNA, not seen in electron density maps, must serve as connecting links between these secondary structural elements and is likely icosahedrally disordered. The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses.

  • Organizational Affiliation

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


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coat proteinB [auth A],
C [auth B],
D [auth C]
189Turnip yellow mosaic virus (Australian isolate)Mutation(s): 3 
Find proteins for P20125 (Turnip yellow mosaic virus (isolate Australia))
Explore P20125 
Go to UniProtKB:  P20125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20125
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*CP*CP*C)-3'A [auth D]3N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 511.53α = 90
b = 511.53β = 90
c = 303.76γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description