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- PDB-5odv: Structure of Watermelon mosaic virus potyvirus. -

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Basic information

Entry
Database: PDB / ID: 5odv
TitleStructure of Watermelon mosaic virus potyvirus.
Components
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
  • coat protein
KeywordsVIRUS / filamentous virus / potyvirus / plant pathogen
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / RNA / Genome polyprotein
Function and homology information
Biological speciesWatermelon mosaic virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsZamora, M. / Mendez-Lopez, E. / Agirrezabala, X. / Cuesta, R. / Lavin, J.L. / Sanchez-Pina, M.A. / Aranda, M. / Valle, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-66326-P Spain
CitationJournal: Sci Adv / Year: 2017
Title: Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses.
Authors: Miguel Zamora / Eduardo Méndez-López / Xabier Agirrezabala / Rebeca Cuesta / José L Lavín / M Amelia Sánchez-Pina / Miguel A Aranda / Mikel Valle /
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. ...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.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: coat protein
a: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
B: coat protein
b: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
C: coat protein
c: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
D: coat protein
d: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
E: coat protein
e: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
F: coat protein
f: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
G: coat protein
g: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
H: coat protein
h: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
I: coat protein
i: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
J: coat protein
j: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
K: coat protein
k: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
L: coat protein
l: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
M: coat protein
m: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
N: coat protein
n: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
O: coat protein
o: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
P: coat protein
p: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Q: coat protein
q: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
R: coat protein
r: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
S: coat protein
s: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
T: coat protein
t: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
U: coat protein
u: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
V: coat protein
v: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
W: coat protein
w: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
X: coat protein
x: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)790,78348
Polymers790,78348
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area190330 Å2
ΔGint-1153 kcal/mol
Surface area251030 Å2
MethodPISA

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Components

#1: Protein ...
coat protein


Mass: 31463.412 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of ...Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of being high flexible regions in the protein.
Source: (natural) Watermelon mosaic virus / References: UniProt: Q70J31
#2: RNA chain ...
RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Watermelon mosaic virus

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Watermelon mosaic virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Watermelon mosaic virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 35 / Used frames/image: 2-27

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Processing

EM software
IDNameVersionCategory
1RELION2.0.3particle selection
4CTFFIND3CTF correction
9RELION2.0.3initial Euler assignment
10RELION2.0.3final Euler assignment
11RELION2.0.3classification
12RELION2.0.33D reconstruction
13Cootmodel refinement
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -40.87 ° / Axial rise/subunit: 3.99 Å / Axial symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50045 / Symmetry type: HELICAL

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