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- PDB-6hxx: Potato virus Y -

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Basic information

Entry
Database: PDB / ID: 6hxx
TitlePotato virus Y
Components
  • Coat protein
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / plant virus / potyvirus / flexible filamentous particle / helical symmetry
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / RNA / Genome polyprotein
Function and homology information
Biological speciesPotato virus Y
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPodobnik, M. / Kezar, A. / Novacek, J. / Polak, M.
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
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / em_entity_assembly_molwt / pdbx_entry_details
Item: _em_admin.last_update / _em_entity_assembly_molwt.id

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Assembly

Deposited unit
AA: Coat protein
Aa: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AB: Coat protein
Ab: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AC: Coat protein
Ac: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AD: Coat protein
Ad: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AE: Coat protein
Ae: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AF: Coat protein
Af: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AG: Coat protein
Ag: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AH: Coat protein
Ah: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AI: Coat protein
Ai: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AJ: Coat protein
Aj: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AK: Coat protein
Ak: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AL: Coat protein
Al: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AM: Coat protein
Am: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AN: Coat protein
An: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AO: Coat protein
Ao: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AP: Coat protein
Ap: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AQ: Coat protein
Aq: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AR: Coat protein
Ar: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AS: Coat protein
As: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AT: Coat protein
At: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AU: Coat protein
Au: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AV: Coat protein
Av: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AW: Coat protein
Aw: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AX: Coat protein
Ax: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AY: Coat protein
Ay: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
AZ: Coat protein
Az: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BA: Coat protein
Ba: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BB: Coat protein
Bb: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BC: Coat protein
Bc: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BD: Coat protein
Bd: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BE: Coat protein
Be: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BF: Coat protein
Bf: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BG: Coat protein
Bg: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BH: Coat protein
Bh: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
BI: Coat protein
Bi: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)1,099,75870
Polymers1,099,75870
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein ...
Coat protein


Mass: 29935.797 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Source: (natural) Potato virus Y / References: UniProt: A0A0A7DJ81
#2: RNA chain ...
RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 35 / Source method: isolated from a natural source
Details: Due to helical averaging during cryo-EM data processing, all nucleotides were assigned the uracil base.
Source: (natural) Potato virus Y
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Potato virus YVIRUSPotato virus Yall0NATURAL
2Coat proteinCOMPLEXApproximately 2000 copies of PVY coat protein assemble around viral ssRNA to form the virion.#11NATURAL
3Viral RNACOMPLEXViral genome consists of positive-sense single stranded RNA.#21NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11
220.29900 MDaNO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Potato virus Y12216NTN
33Potato virus Y12216NTN
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSTRAINVIRION
22
33
Natural hostOrganism: Solanum tuberosum
Buffer solutionpH: 8
Buffer componentConc.: 5 mM / Name: disodium tetraborate / Formula: B4Na2O7
SpecimenConc.: 0.9 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: 726
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf1.05CTF correction
7Coot0.8.8model fitting
8UCSF Chimera1.11.2model fitting
12RELION2.1classification
13RELION2.13D reconstruction
14PHENIX1.13.2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -40.95 ° / Axial rise/subunit: 3.95 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 215123
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162213 / Symmetry type: HELICAL

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