1F2N

RICE YELLOW MOTTLE VIRUS

• PDB DOI: https://doi.org/10.2210/pdb1F2N/pdb

• Classification: VIRUS
• Organism(s): Rice yellow mottle virus
• Mutation(s): No 


• Deposited: 2000-05-26 Released: 2000-11-01 
• Deposition Author(s): Qu, C., Liljas, L., Opalka, N., Brugidou, C., Yeager, M., Beachy, R.N., Fauquet, C.M., Johnson, J.E., Lin, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.218 
• R-Value Observed: 0.227 

Literature

3D domain swapping modulates the stability of members of an icosahedral virus group.

Qu, C., Liljas, L., Opalka, N., Brugidou, C., Yeager, M., Beachy, R.N., Fauquet, C.M., Johnson, J.E., Lin, T.

(2000) Structure 8: 1095-1103

• PubMed: 11080631 
• DOI: https://doi.org/10.1016/s0969-2126(00)00508-6
• Primary Citation of Related Structures:  
  1F2N


• PubMed Abstract: 
  

  Rice yellow mottle virus (RYMV) is a major pathogen that dramatically reduces rice production in many African countries. RYMV belongs to the genus sobemovirus, one group of plant viruses with icosahedral capsids and single-stranded, positive-sense RNA genomes.

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Organizational Affiliation: 

Department of Molecular Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Macromolecule Content

• Total Structure Weight: 78.15 kDa 
• Atom Count: 4,730 
• Modelled Residue Count: 590 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN	A, B, C	238	Rice yellow mottle virus	Mutation(s): 0
UniProt
Find proteins for Q86527 (Rice yellow mottle virus) Explore Q86527  Go to UniProtKB:  Q86527

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth B], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.218 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 283.5	α = 90
b = 401.8	β = 89.4
c = 284	γ = 90

Software Package:

Software Name	Purpose
GLRF	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-01 
Deposition Author(s): Qu, C., Liljas, L., Opalka, N., Brugidou, C., Yeager, M., Beachy, R.N., Fauquet, C.M., Johnson, J.E., Lin, T.

Revision History  

• Version 1.0: 2000-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations