1A34

SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 37-59

  • DOI: 10.1006/jmbi.1997.1570
  • Primary Citation of Related Structures:  
    1A34

  • PubMed Abstract: 
  • The molecular structure of satellite tobacco mosaic virus (STMV) has been refined to 1.8 A resolution using X-ray diffraction data collected from crystals grown in microgravity. The final R value was 0.179 and Rfree was 0.184 for 219,086 independent reflections ...

    The molecular structure of satellite tobacco mosaic virus (STMV) has been refined to 1.8 A resolution using X-ray diffraction data collected from crystals grown in microgravity. The final R value was 0.179 and Rfree was 0.184 for 219,086 independent reflections. The final model of the asymmetric unit contained amino acid residues 13 to 159 of a coat protein monomer, 21 nucleotides, a sulfate ion, and 168 water molecules. The nucleotides were visualized as 30 helical segments of nine base-pairs with an additional base stacked at each 3' end, plus a "free" nucleotide, not belonging to the helical segments, but firmly bound by the protein. Sulfate ions are located exactly on 5-fold axes and each is coordinated by ten asparagine side-chains. Of the 10,080 structural waters, 168 per asymmetric unit, about 20% serve to bridge the macromolecular components at protein-protein and protein-nucleic acid interfaces. Binding of RNA to the protein involves some salt linkages, particularly to the phosphate of the free nucleotide, but the major contribution is from an intricate network of hydrogen bonds. There are numerous water molecules in the RNA-protein interface, many serving as intermediate hydrogen bond bridges. The sugar-phosphate backbone contributes most of the donors and acceptors for the RNA. The helical RNA conformation is nearest that of A form DNA. The central region of a helical segment is most extensively involved in contacts with protein, and exhibits low thermal parameters which increase dramatically toward the ends. The visible RNA represents approximately 59% of the total nucleic acid in the virion and is derived from the single-stranded genome, which has folded upon itself to form helical segments. Linking of the helices and the free nucleotides in a contiguous and efficient manner severely restricts the disposition of the remaining, unseen nucleic acid. Using the remaining nucleotides it is possible to fold the RNA according to motifs that provide a periodic distribution of RNA structural elements compatible with the icosahedrally symmetrical arrangement seen in the crystallographic structure. The intimate relationship between protein and nucleic acid in STMV suggests an assembly pathway based on the cooperative and coordinated co-condensation of RNA with capsid protein dimers.


    Related Citations: 
    • 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
    • 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
    • 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 Biochemistry, University of California, Riverside, CA 92521, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)A159Satellite tobacco mosaic virusMutation(s): 0 
UniProt
Find proteins for P17574 (Satellite tobacco mosaic virus)
Explore P17574 
Go to UniProtKB:  P17574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17574
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')B 10N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')C 10N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U
Query on U

Download Ideal Coordinates CCD File 
E [auth B]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.27α = 90
b = 191.77β = 90
c = 202.5γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
BRICOGNE'Smodel building
INTERPOLATEmodel building
TNTrefinement
HEAVYmodel building
SDMSdata reduction
SDMSdata scaling
HEAVYphasing
BRICOGNE'Sphasing
INTERPOLATEphasing
TNTphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Other, Source and taxonomy
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description