2BUK

SATELLITE TOBACCO NECROSIS VIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Satellite Tobacco Necrosis Virus After Crystallographic Refinement at 2.5 A Resolution.

Jones, T.A.Liljas, L.

(1984) J.Mol.Biol. 177: 735


  • PubMed Abstract: 
  • The structure of the protein subunit of satellite tobacco necrosis virus has been solved at 3.7 A resolution. We have now crystallographically refined the original model and extended the resolution ot 2.5 A in order to get a model accurate enough to ...

    The structure of the protein subunit of satellite tobacco necrosis virus has been solved at 3.7 A resolution. We have now crystallographically refined the original model and extended the resolution ot 2.5 A in order to get a model accurate enough to explain the details of the subunit interactions. The refinement was done with a novel method utilizing the icosahedral symmetry of the virus particle. The final model shows a complicated network of interactions, involving salt linkages, hydrogen bonds and hydrophobic contacts. In addition, we have located three different metal ion sites in the protein shell, linking the protein subunits together. These sites are probably occupied by calcium ions. One site is found in a general position near the icosahedral 3-fold axis of the virus. The ligands form an octahedral arrangement, with two main chain carbonyl oxygens (0-61 and 0-64), one carboxylate oxygen (OD1 from Asp194) of the same subunit and a second carboxylate oxygen (OE1 of Glu25) from a 3-fold related subunit. Two water molecules complete the octahedral arrangement. A second site is on the icosahedral 3-fold axis and is liganded by the carboxylate oxygens of the 3-fold related Asp55 residues. The third metal ion site is found on the 5-fold axis, liganded by the five carbonyl oxygens of Thr138 and two water molecules. We are unable to locate the first 11 N-terminal amino acid residues, which point into the virus interior. No interpretable density for RNA has been found, indicating that the nucleic acid of the virus does not have a unique orientation in the crystal.


    Related Citations: 
    • Crystallographic Refinement of Macromolecules Having Non-Crystallographic Symmetry
      Jones, T.A.,Liljas, L.
      (1984) Acta Crystallogr.,Sect.A 40: 50
    • Structure of Satellite Tobacco Necrosis Virus at 3.0 Angstroms Resolution
      Liljas, L.,Unge, T.,Jones, T.A.,Fridborg, K.,Lovgren, S.,Skoglund, U.,Strandberg, B.
      (1982) J.Mol.Biol. 159: 93



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN
A
196Satellite tobacco necrosis virus 1Mutation(s): 0 
Find proteins for P03606 (Satellite tobacco necrosis virus 1)
Go to UniProtKB:  P03606
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Work: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 317.270α = 90.00
b = 304.030β = 94.36
c = 184.600γ = 90.00
Software Package:
Software NamePurpose
FRODOrefinement
FILMEdata reduction
PURDUEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-06-14 
  • Released Date: 2005-08-18 
  • Deposition Author(s): Jones, T.A., Liljas, L.
  • This entry supersedes: 2STV

Revision History 

  • Version 1.0: 2005-08-18
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Derived calculations, Other, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection