1LAJ

The Structure of Tomato Aspermy Virus by X-Ray Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of Tomato Aspermy Virus by X-Ray Crystallography

Lucas, R.W.Larson, S.B.Canady, M.A.McPherson, A.

(2002) J.STRUCT.BIOL. 139: 90-102


  • PubMed Abstract: 
  • The three-dimensional structure of tomato aspermy virus (TAV) has been solved by X-ray crystallography and refined to an R factor of 0.218 for 3.4-40 A data (effective resolution of 4A). Molecular replacement, using cucumber mosaic virus (Smith et al ...

    The three-dimensional structure of tomato aspermy virus (TAV) has been solved by X-ray crystallography and refined to an R factor of 0.218 for 3.4-40 A data (effective resolution of 4A). Molecular replacement, using cucumber mosaic virus (Smith et al., 2000), provided phases for the initial maps used for model building. The coat protein of the 280 A diameter virion has the canonical "Swiss roll" beta-barrel topology with a distinctive amino-terminal alpha-helix directed into the interior of the virus where it interacts with encapsidated RNA. The N-terminal helices are joined to the beta-barrels of protein subunits by extended polypeptides of six amino acids, which serve as flexible hinges allowing movement of the helices in response to local RNA distribution. Segments of three nucleotides of partially disordered RNA interact with the capsid, primarily through arginine residues, at interfaces between A and B subunits. Side chains of cys64 and cys106 form the first disulfide observed in a cucumovirus, including a unique cysteine, 106, in a region otherwise conserved. A positive ion, putatively modeled as a Mg(+)ion, lies on the quasi-threefold axis surrounded by three quasi-symmetric glutamate 175 side chains.


    Related Citations: 
    • Preliminary X-ray Diffraction Analysis of Crystals of Tomato aspermy virus (TAV)
      Canady, M.A.,Leja, C.A.,Day, J.,McPherson, A.
      (1995) Proteins 21: 265


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
capsid protein
A, B, C
217Tomato aspermy virusN/A
Find proteins for P23627 (Tomato aspermy virus)
Go to UniProtKB:  P23627
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*AP*AP*A)-3'R3N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.218 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 294.296α = 90.00
b = 327.393β = 90.00
c = 382.066γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance