5ODV | pdb_00005odv

Structure of Watermelon mosaic virus potyvirus.

• PDB DOI: https://doi.org/10.2210/pdb5ODV/pdb
• EM Map EMD-3785: EMDB EMDataResource
• NAKB: 5ODV

• Classification: VIRUS
• Organism(s): Watermelon mosaic virus
• Mutation(s): No 


• Deposited: 2017-07-06 Released: 2017-09-27 
• Deposition Author(s): Zamora, M., Mendez-Lopez, E., Agirrezabala, X., Cuesta, R., Lavin, J.L., Sanchez-Pina, M.A., Aranda, M., Valle, M.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses.

Zamora, M., Mendez-Lopez, E., Agirrezabala, X., Cuesta, R., Lavin, J.L., Sanchez-Pina, M.A., Aranda, M.A., Valle, M.

(2017) Sci Adv 3: eaao2182-eaao2182

• PubMed: 28948231 
• DOI: https://doi.org/10.1126/sciadv.aao2182
• Primary Citation Related Structures: 
  5ODV


• PubMed Abstract: 
  

  Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza viruses.

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Organizational Affiliation: 
• Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain.
Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 790.78 kDa 
• Atom Count: 42,288 
• Modeled Residue Count: 5,088 
• Deposited Residue Count: 6,864 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
coat protein	A, AA [auth N], C [auth B], CA [auth O], E [auth C], EA [auth P], G [auth D], GA [auth Q], I [auth E], IA [auth R], K [auth F], KA [auth S], M [auth G], MA [auth T], O [auth H], OA [auth U], Q [auth I], QA [auth V], S [auth J], SA [auth W], U [auth K], UA [auth X], W [auth L], Y [auth M]	281	Watermelon mosaic virus	Mutation(s): 0
UniProt
Find proteins for Q70J31 (Watermelon mosaic virus) Explore Q70J31  Go to UniProtKB:  Q70J31

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*UP*U)-3')	B [auth a], BA [auth n], D [auth b], DA [auth o], F [auth c], FA [auth p], H [auth d], HA [auth q], J [auth e], JA [auth r], L [auth f], LA [auth s], N [auth g], NA [auth t], P [auth h], PA [auth u], R [auth i], RA [auth v], T [auth j], TA [auth w], V [auth k], VA [auth x], X [auth l], Z [auth m]	5	Watermelon mosaic virus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0.3
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX	1.11.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Zamora, M., Mendez-Lopez, E., Agirrezabala, X., Cuesta, R., Lavin, J.L., Sanchez-Pina, M.A., Aranda, M., Valle, M.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2015-66326-P

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references