1C8N

TOBACCO NECROSIS VIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of tobacco necrosis virus at 2.25 A resolution.

Oda, Y.Saeki, K.Takahashi, Y.Maeda, T.Naitow, H.Tsukihara, T.Fukuyama, K.

(2000) J.Mol.Biol. 300: 153-169

  • DOI: 10.1006/jmbi.2000.3831

  • PubMed Abstract: 
  • The crystal structure of tobacco necrosis virus (TNV) has been determined by real-space averaging with 5-fold non-crystallographic symmetry, and refined to R=25.3 % for diffraction data to 2.25 A resolution. A total of 180 subunits form a T=3 virus s ...

    The crystal structure of tobacco necrosis virus (TNV) has been determined by real-space averaging with 5-fold non-crystallographic symmetry, and refined to R=25.3 % for diffraction data to 2.25 A resolution. A total of 180 subunits form a T=3 virus shell with a diameter of about 280 A and a small protrusion at the 5-fold axis. In 276 amino acid residues, the respective amino terminal 86, 87 and 56 residues of the A, B and C subunits are disordered. No density for the RNA was found. The subunits have a "jelly roll" beta-barrel structure, as have the structures of the subunits of other spherical viruses. The tertiary and quaternary structures of TNV are, in particular, similar to those of southern bean mosaic virus, although they are classified in different groups. Invisible residues 1 to 56 with a high level of basic residues are considered to be located inside the particle. Sequence comparison of the coat proteins of several TNV strains showed that the sequences of the disordered segment diverge considerably as compared with those of the ordered segment, consistent with a small tertiary structural constraint being imposed on the N-terminal segment. Basic residues are localized on the subunit interfaces or inner surface of the capsid. Positive charges of the basic residues facing the interior, as well as those of the N-terminal segment, may neutralize the negative charge of the RNA inside. Five calcium ions per icosahedral asymmetric unit are located at the subunit interfaces; three are close to the exterior surface, the other two away from it. The environments of the first three are similar, and those of the other two sites are similar. These calcium ions are assumed to be responsible for the stabilization/transition of the quaternary structure of the shell. Three peptide segments ordered only in the C subunits are clustered around each 3-fold (quasi-6-fold) axis forming a beta-annulus, and may lead to quasi-equivalent interactions for the organization of the T=3 shell.


    Related Citations: 
    • Symmetry and Subunit Arrangement of Tobacco Necrosis Virus (TNV)
      Tsukihara, T.,Yokota, Y.,Koyama, T.,Fukuyama, K.,Matsubara, H.
      (1990) Acta Crystallogr.,Sect.B 46: 855
    • Crystal Structural Analysis of Tobacco Necrosis Virus at 5 Angstrom Resolution
      Bando, M.,Morimoto, Y.,Sato, T.,Tsukihara, T.,Yokota, Y.,Fukuyama, K.,Matsubara, H.
      (1994) Acta Crystallogr.,Sect.D 50: 878
    • Crystallization and Preliminary X-Ray Diffraction Studies of Tobacco Necrosis Virus
      Fukuyama, K.,Hirota, S.,Tsukihara, T.
      (1987) J.Mol.Biol. 196: 961


    Organizational Affiliation

    Department of Biology Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN
A, B, C
276Tobacco necrosis virus (Toyama)Gene Names: cp1
Find proteins for Q9IPS9 (Tobacco necrosis virus (Toyama))
Go to UniProtKB:  Q9IPS9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.253 
  • Space Group: P 42 3 2
Unit Cell:
Length (Å)Angle (°)
a = 336.400α = 90.00
b = 336.400β = 90.00
c = 336.400γ = 90.00
Software Package:
Software NamePurpose
DMmodel building
X-PLORrefinement
CCP4data scaling
DENZOdata reduction
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-05-20 
  • Released Date: 2000-08-30 
  • Deposition Author(s): Oda, Y., Fukuyama, K.

Revision History 

  • Version 1.0: 2000-08-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance