1PGL

BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus.

Lin, T.Cavarelli, J.Johnson, J.E.

(2003) Virology 314: 26-33

  • DOI: 10.1016/s0042-6822(03)00457-4
  • Primary Citation of Related Structures:  
    1PGL, 1PGW

  • PubMed Abstract: 
  • Ordered nucleic acid in an icosahedral virus was first visualized in the X-ray structure of the Picorna-like plant virus, Bean pod mottle virus (BPMV). Virus particles containing the 3500 nucleotide segment of the BPMV bipartite RNA genome (middle component) had nearly 20% of the genome ordered ...

    Ordered nucleic acid in an icosahedral virus was first visualized in the X-ray structure of the Picorna-like plant virus, Bean pod mottle virus (BPMV). Virus particles containing the 3500 nucleotide segment of the BPMV bipartite RNA genome (middle component) had nearly 20% of the genome ordered. Here we report the refined structures of the middle component, bottom component (particles containing the 5800 nucleotide segment of the genome), and top component (empty particles of BPMV capsid protein). The bottom component particles contain ordered RNA in the same location as middle component. Although the ordered RNA density in both nucleoprotein particles is the average of the contents of 60 icosahedral asymmetric units, both nucleoprotein components show that the base density for the first two nucleotides is predominantly purine, while the next five appear to be predominantly pyrimidine. The empty capsid demonstrates that RNA dictates the order of the N-terminal 19 residues of the large subunit because these residues are invisible in the top component.


    Related Citations: 
    • Protein-/RNA Interactions in an Icosahedral Virus at 3.0 Angstroms Resolution
      Chen, Z., Stauffacher, C., Li, Y., Schmidt, T., Bomu, W., Kamer, G., Shanks, M., Lomonossoff, G., Johnson, J.E.
      (1989) Science 245: 154

    Organizational Affiliation

    Department of Molecular Biology and Center for Integrative Molecular Biosciences, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BEAN POD MOTTLE VIRUS SMALL (S) SUBUNITB [auth 1]185Bean-pod mottle virus (strain Kentucky G7)Mutation(s): 0 
UniProt
Find proteins for P23009 (Bean-pod mottle virus (strain Kentucky G7))
Explore P23009 
Go to UniProtKB:  P23009
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
BEAN POD MOTTLE VIRUS LARGE (L) SUBUNITC [auth 2]370Bean-pod mottle virus (strain Kentucky G7)Mutation(s): 0 
UniProt
Find proteins for P23009 (Bean-pod mottle virus (strain Kentucky G7))
Explore P23009 
Go to UniProtKB:  P23009
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*GP*UP*CP*UP*C)-3'A [auth 3]6N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Work: 0.196 
    • R-Value Observed: 0.196 
    • Space Group: P 2 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 311.2α = 90
    b = 284.2β = 90
    c = 350.5γ = 90
    Software Package:
    Software NamePurpose
    MGROSCdata collection
    MGROSCdata reduction
    X-PLORrefinement
    MGROSCdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2003-11-18
      Type: Initial release
    • Version 1.1: 2008-04-29
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-10-11
      Changes: Refinement description