1PGL

BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 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

  • Primary Citation of Related Structures:  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 co ...

    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
1
185Bean-pod mottle virus (strain Kentucky G7)N/A
Find proteins for P23009 (Bean-pod mottle virus (strain Kentucky G7))
Go to UniProtKB:  P23009
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
2
370Bean-pod mottle virus (strain Kentucky G7)N/A
Find proteins for P23009 (Bean-pod mottle virus (strain Kentucky G7))
Go to UniProtKB:  P23009
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*AP*GP*UP*CP*UP*C)-3'36N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.196 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 311.200α = 90.00
b = 284.200β = 90.00
c = 350.500γ = 90.00
Software Package:
Software NamePurpose
MGROSCdata reduction
MGROSCdata collection
MGROSCdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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