5FN1 | pdb_00005fn1

Electron cryo-microscopy of filamentous flexible virus PepMV (Pepino Mosaic Virus)

• PDB DOI: https://doi.org/10.2210/pdb5FN1/pdb
• EM Map EMD-3236: EMDB EMDataResource
• NAKB: 5FN1

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


• Deposited: 2015-11-10 Released: 2015-12-30 
• Deposition Author(s): Agirrezabala, X., Mendez-Lopez, E., Lasso, G., Sanchez-Pina, M.A., Aranda, M.A., Valle, M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses.

Agirrezabala, X., Mendez-Lopez, E., Lasso, G., Sanchez-Pina, M.A., Aranda, M., Valle, M.

(2015) Elife 4: e11795-e11795

• PubMed: 26673077 
• DOI: https://doi.org/10.7554/eLife.11795
• Primary Citation Related Structures: 
  5FN1


• PubMed Abstract: 
  

  Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies - a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses.

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Organizational Affiliation: 
• Structural Biology Unit, Center for Cooperative Research in Biosciences, Derio, Spain.
Centro de Edafología y Biología Aplicada del Segura, Murcia, Spain.
Consejo Superior de Investigaciones Científicas, Murcia, Spain.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 18-mer - A18 

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

Macromolecule Content 

• Total Structure Weight: 26.63 kDa 
• Atom Count: 1,735 
• Modeled Residue Count: 222 
• Deposited Residue Count: 242 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAT PROTEIN	A	237	Pepino mosaic virus	Mutation(s): 0
UniProt
Find proteins for Q71FK2 (Pepino mosaic virus) Explore Q71FK2  Go to UniProtKB:  Q71FK2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*UP*UP*UP)-3'	B	5	Pepino mosaic virus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	SPRING

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Agirrezabala, X., Mendez-Lopez, E., Lasso, G., Sanchez-Pina, M.A., Aranda, M.A., Valle, M.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations