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- PDB-6hxz: Virus-like Particles based on Potato Virus Y -

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Basic information

Entry
Database: PDB / ID: 6hxz
TitleVirus-like Particles based on Potato Virus Y
ComponentsPolyprotein
KeywordsVIRUS LIKE PARTICLE / Virus-like Particle / Potyvirus / flexuous filaments / stacked-ring assembly
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / serine-type peptidase activity / helicase activity / vesicle / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / serine-type peptidase activity / helicase activity / vesicle / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPotato virus Y
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPodobnik, M. / Kezar, A. / Novacek, J.
Funding support Slovenia, Czech Republic, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Slovenian Research AgencyJ7-7248 Slovenia
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structural basis for the multitasking nature of the potato virus Y coat protein.
Authors: Andreja Kežar / Luka Kavčič / Martin Polák / Jiří Nováček / Ion Gutiérrez-Aguirre / Magda Tušek Žnidarič / Anna Coll / Katja Stare / Kristina Gruden / Maja Ravnikar / David ...Authors: Andreja Kežar / Luka Kavčič / Martin Polák / Jiří Nováček / Ion Gutiérrez-Aguirre / Magda Tušek Žnidarič / Anna Coll / Katja Stare / Kristina Gruden / Maja Ravnikar / David Pahovnik / Ema Žagar / Franci Merzel / Gregor Anderluh / Marjetka Podobnik /
Abstract: Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously ...Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
History
DepositionOct 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1May 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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Assembly

Deposited unit
a: Polyprotein
b: Polyprotein
c: Polyprotein
d: Polyprotein
e: Polyprotein
f: Polyprotein
g: Polyprotein
h: Polyprotein
i: Polyprotein
j: Polyprotein
k: Polyprotein
l: Polyprotein
m: Polyprotein
n: Polyprotein
o: Polyprotein
p: Polyprotein
q: Polyprotein
r: Polyprotein
s: Polyprotein
t: Polyprotein
u: Polyprotein
v: Polyprotein
w: Polyprotein
x: Polyprotein


Theoretical massNumber of molelcules
Total (without water)718,45924
Polymers718,45924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: equilibrium centrifugation, Particles isolated from specific gradient fractions., gel filtration, Retention time indicating high molecular weight complexes., microscopy, Long flexible ...Evidence: equilibrium centrifugation, Particles isolated from specific gradient fractions., gel filtration, Retention time indicating high molecular weight complexes., microscopy, Long flexible filaments visible with negative stain TEM and cryo-EM., native gel electrophoresis, Bands at high molecular weight indicating big complexes.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area102980 Å2
ΔGint-452 kcal/mol
Surface area207970 Å2
MethodPISA

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Components

#1: Protein ...
Polyprotein


Mass: 29935.797 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato virus Y / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C4URS3

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Virus-like Particle based on Potato Virus YCOMPLEXRecombinantly expressed coat protein self-assembles into virus-like particles.all0RECOMBINANT
2Coat protein of Potato Virus YCOMPLEXall1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11
220.29900 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Potato virus Y12216NTN
32Potato virus Y12216NTN
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
21Escherichia coli (E. coli)562BL21(DE3)pT7-7
32Escherichia coli (E. coli)562BL21(DE3)pT7-7
Buffer solutionpH: 7.4 / Details: 140 mM NaCl 2.7 mM KCl
Buffer componentConc.: 12 mM / Name: Phosphate buffered saline / Formula: PBS
SpecimenConc.: 6.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 5344
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2helixboxer.py
2EPUimage acquisition
4Gctf1.05CTF correction
7Coot0.8.8model fitting
8UCSF Chimera1.11.2model fitting
10PHENIX1.13.2998model refinement
13RELION2classification
14RELION2.1classification
15RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 13.24 ° / Axial rise/subunit: 42.65 Å / Axial symmetry: C8
Particle selectionNum. of particles selected: 244988
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148876 / Symmetry type: HELICAL

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