4NIA

Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Satellite tobacco mosaic virus refined to 1.4 angstrom resolution.

Larson, S.B.Day, J.S.McPherson, A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2316-2330

  • DOI: 10.1107/S1399004714013789
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Satellite tobacco mosaic virus (STMV) is among the smallest viruses, having 60 identical subunits arranged with T = 1 icosahedral symmetry. Its crystal structure was solved at 290 K and was refined using, in part, crystals grown in microgravity. Elec ...

    Satellite tobacco mosaic virus (STMV) is among the smallest viruses, having 60 identical subunits arranged with T = 1 icosahedral symmetry. Its crystal structure was solved at 290 K and was refined using, in part, crystals grown in microgravity. Electron-density maps revealed nearly 57% of the genomic ssRNA. Using six flash-cooled crystals, diffraction data were recorded to 1.4 Å resolution and independent refinements of the STMV model were carried out versus the previous 1.8 Å resolution data representing merged data from 21 crystals (271,689 unique reflections), data consisting of corresponding reflections to 1.8 Å resolution from the cooled crystals and 1.4 Å resolution data from the cooled crystals comprised of 570,721 unique reflections. Models were independently refined with full NCS constraints using the program CNS and in restrained mode using the programs CNS, REFMAC5 and SHELX-97, with the latter two procedures including anisotropic temperature factors. Significant additional structural detail emerged from the analyses, including a unique cation and anion arrangement on fivefold axes and a precise assessment of icosahedral symmetry exactness in the crystal lattice. STMV represents the highest resolution native virus structure currently known by a substantial margin, and it permits the evaluation of a precise atomic model of a spherical virus at near-atomic resolution for the first time.


    Related Citations: 
    • Refined structure of satellite tobacco mosaic virus at 1.8 A resolution.
      Larson, S.B., Day, J., Greenwood, A., McPherson, A.
      (1998) J Mol Biol 277: 37
    • Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution.
      Larson, S.B., Koszelak, S., Day, J., Greenwood, A., Dodds, J.A., McPherson, A.
      (1993) J Mol Biol 231: 375
    • Double-helical RNA in satellite tobacco mosaic virus.
      Larson, S.B., Koszelak, S., Day, J., Greenwood, A., Dodds, J.A., McPherson, A.
      (1993) Nature 361: 179
    • Macromolecular crystal growth experiments on International Microgravity Laboratory--1.
      Day, J., McPherson, A.
      (1992) Protein Sci 1: 1254
    • Preliminary analysis of crystals of satellite tobacco mosaic virus.
      Koszelak, S., Dodds, J.A., McPherson, A.
      (1989) J Mol Biol 209: 323

    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: 1
MoleculeChainsSequence LengthOrganismDetails
Coat protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
159Satellite tobacco mosaic virusMutation(s): 0 
Find proteins for P17574 (Satellite tobacco mosaic virus)
Go to UniProtKB:  P17574
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')P, Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d10Satellite tobacco mosaic virus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')e, f,g,h,i,j,k,l,m,n,o,p,q,r,s10Satellite tobacco mosaic virus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*U)-3')1, 2,3,4,5,6,7,8,t,u,v,w,x,y,z2Satellite tobacco mosaic virus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
C, H, K
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, F, K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.268α = 90
b = 191.774β = 90
c = 202.503γ = 90
Software Package:
Software NamePurpose
SDMSdata collection
REFMACrefinement
SDMSdata reduction
SDMSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description