1BMV | pdb_00001bmv

PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1BMV/pdb
• NAKB: 1BMV

• Classification: Virus/RNA
• Organism(s): Bean pod mottle virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1989-10-09 Released: 1989-10-09 
• Deposition Author(s): Chen, Z., Stauffacher, C., Li, Y., Schmidt, T., Bomu, W., Kamer, G., Shanks, M., Lomonossoff, G., Johnson, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 
  0.326 (DCC) 
• R-Value Observed: 
  0.330 (Depositor) 

Literature

Protein-RNA interactions in an icosahedral virus at 3.0 A resolution.

Chen, Z.G., Stauffacher, C., Li, Y., Schmidt, T., Bomu, W., Kamer, G., Shanks, M., Lomonossoff, G., Johnson, J.E.

(1989) Science 245: 154-159

• PubMed: 2749253 
• DOI: https://doi.org/10.1126/science.2749253
• Primary Citation Related Structures: 
  1BMV


• PubMed Abstract: 
  

  Nearly 20 percent of the packaged RNA in bean-pod mottle virus (BPMV) binds to the capsid interior in a symmetric fashion and is clearly visible in the electron density map. The RNA displaying icosahedral symmetry is single-stranded with well-defined polarity and stereochemical properties. Interactions with protein are dominated by nonbonding forces with few specific contacts. The tertiary and quaternary structures of the BPMV capsid proteins are similar to those observed in animal picornaviruses, supporting the close relation between plant comoviruses and animal picornaviruses established by previous biological studies.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 66.67 kDa 
• Atom Count: 4,613 
• Modeled Residue Count: 570 
• Deposited Residue Count: 583 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)	B [auth 1]	198	Bean pod mottle virus	Mutation(s): 0
UniProt
Find proteins for P23009 (Bean-pod mottle virus (strain Kentucky G7)) Explore P23009  Go to UniProtKB:  P23009

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)	C [auth 2]	374	Bean pod mottle virus	Mutation(s): 0
UniProt
Find proteins for P23009 (Bean-pod mottle virus (strain Kentucky G7)) Explore P23009  Go to UniProtKB:  P23009

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')	A [auth M]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work:  0.326 (DCC) 
• R-Value Observed: 0.330 (Depositor) 

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
NONE	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1989-10-09 
Deposition Author(s): Chen, Z., Stauffacher, C., Li, Y., Schmidt, T., Bomu, W., Kamer, G., Shanks, M., Lomonossoff, G., Johnson, J.E.

Revision History  

• Version 1.0: 1989-10-09
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2023-04-19
  Type: Remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.1: 2024-05-22
  Changes: Data collection