1VTM | pdb_00001vtm

STRUCTURE OF THE U2 STRAIN OF TOBACCO MOSAIC VIRUS REFINED AT 3.5 ANGSTROMS RESOLUTION USING X-RAY FIBER DIFFRACTION

• PDB DOI: https://doi.org/10.2210/pdb1VTM/pdb
• NAKB: 1VTM

• Classification: Virus/RNA
• Organism(s): Tobacco mild green mosaic virus
• Mutation(s): No 


• Deposited: 1992-03-30 Released: 1994-07-31 
• Deposition Author(s): Stubbs, G., Pattanayek, R.

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Experimental Data Snapshot

• Method: FIBER DIFFRACTION
• Resolution: 3.50 Å
• R-Value Observed: 
  0.096 (Depositor) 

Literature

Structure of the U2 strain of tobacco mosaic virus refined at 3.5 A resolution using X-ray fiber diffraction.

Pattanayek, R., Stubbs, G.

(1992) J Mol Biology 228: 516-528

• PubMed: 1453461 
• DOI: https://doi.org/10.1016/0022-2836(92)90839-c
• Primary Citation Related Structures: 
  1VTM


• PubMed Abstract: 
  

  The structure of the U2 strain of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 3.5 A resolution, and refined by a combination of restrained least-squares and molecular dynamics methods to an R-factor of 0.096. The structure is extremely similar to that of the common strain of TMV, with the largest differences being in the protein loop that makes up the inner surface of the virus, and in the C-terminal region on the outer surface. Differences in the inner loop can be correlated with differences in the properties of the two viruses.

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Organizational Affiliation: 
• Department of Molecular Biology Vanderbilt University, Nashville, TN 37235.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 49-mer - A49 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 18.43 kDa 
• Atom Count: 1,307 
• Modeled Residue Count: 161 
• Deposited Residue Count: 161 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	B [auth P]	158	Tobacco mild green mosaic virus	Mutation(s): 0  Gene Names: CP
UniProt
Find proteins for P03579 (Tobacco mild green mosaic virus) Explore P03579  Go to UniProtKB:  P03579

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*AP*A)-3')	A [auth R]	3	Tobacco mild green mosaic virus

Experimental Data & Validation

Experimental Data

• Method: FIBER DIFFRACTION
• Resolution: 3.50 Å
• R-Value Observed: 0.096 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 1	α = 90
b = 1	β = 90
c = 1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-07-31 
Deposition Author(s): Stubbs, G., Pattanayek, R.

Revision History  

• Version 1.0: 1994-07-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations