2FZ2

Structure of Turnip Yellow Mosaic Virus at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.virol.2005.01.036
  • Primary Citation of Related Structures:  2FZ1

  • 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 t ...

    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.


    Related Citations: 
    • Crystal structure of an empty capsid of turnip yellow mosaic virus.
      van Roon, A.M.,Bink, H.H.,Plaisier, J.R.,Pleij, C.W.,Abrahams, J.P.,Pannu, N.S.
      (2004) J.Mol.Biol. 341: 1205
    • Crystal structure of turnip yellow mosaic virus.
      Canady, M.A.,Larson, S.B.,Day, J.,McPherson, A.
      (1996) Nat.Struct.Mol.Biol. 3: 771
    • Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV).
      Canady, M.A.,Day, J.,McPherson, A.
      (1995) Proteins 21: 78


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coat protein
A, B, C
189Turnip yellow mosaic virusN/A
Find proteins for P20125 (Turnip yellow mosaic virus)
Go to UniProtKB:  P20125
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*CP*C)-3'D3N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 511.530α = 90.00
b = 511.530β = 90.00
c = 303.760γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance