Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 120-mer - A60B60 

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

Macromolecule Content

• Total Structure Weight: 59.31 kDa 
• Atom Count: 4306 
• Modelled Residue Count: 536 
• Deposited Residue Count: 536 
• Unique protein chains: 2

1PGW

BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT

• PDB DOI: 10.2210/pdb1PGW/pdb

• Classification: VIRUS
• Organism(s): Bean-pod mottle virus (strain Kentucky G7)
• Mutation(s): No 


• Deposited: 2003-05-28 Released: 2003-11-18 
• Deposition Author(s): Lin, T., Cavarelli, J., Johnson, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

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

• PubMed: 14517057 
• 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. 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.

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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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT	A [auth 1]	185	Bean-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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT	B [auth 2]	351	Bean-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 311.2	α = 90
b = 284.2	β = 90
c = 350.5	γ = 90

Software Package:

Software Name	Purpose
MGROSC	data collection
MGROSC	data reduction
X-PLOR	refinement
MGROSC	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-28 
• Released Date: 2003-11-18 
Deposition Author(s): Lin, T., Cavarelli, J., Johnson, J.E.

Revision History  

• 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