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- PDB-6r7g: Atomic structure of potato virus X, the prototype of the Alphafle... -

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Basic information

Entry
Database: PDB / ID: 6r7g
TitleAtomic structure of potato virus X, the prototype of the Alphaflexiviridae family
Components
  • Coat protein
  • polyU RNA
KeywordsVIRUS / Coat Protein / RNA
Function / homology
Function and homology information


helical viral capsid / ribonucleoprotein complex / structural molecule activity
Similarity search - Function
Potexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Coat protein / Coat protein
Similarity search - Component
Biological speciesPotato virus X
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsGrinzato, A. / Kandiah, E. / Lico, C. / Betti, C. / Baschieri, S. / Zanotti, G.
CitationJournal: Nat Chem Biol / Year: 2020
Title: Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family.
Authors: Alessandro Grinzato / Eaazhisai Kandiah / Chiara Lico / Camilla Betti / Selene Baschieri / Giuseppe Zanotti /
Abstract: Potato virus X (PVX) is a positive-sense single-stranded RNA (ssRNA) filamentous plant virus belonging to the Alphaflexiviridae family, considered in recent years as a tool for nanotechnology ...Potato virus X (PVX) is a positive-sense single-stranded RNA (ssRNA) filamentous plant virus belonging to the Alphaflexiviridae family, considered in recent years as a tool for nanotechnology applications. We present the cryo-electron microscopy structure of the PVX particle at a resolution of 2.2 Å. The well-defined density of the coat proteins and of the genomic RNA allowed a detailed analysis of protein-RNA interactions, including those mediated by solvent molecules. The particle is formed by repeated segments made of 8.8 coat proteins, forming a left-handed helical structure. The RNA runs in an internal crevice along the virion, packaged in 5-nucleotide repeats in which the first four bases are stacked in the classical way, while the fifth is rotated and nearly perpendicular. The resolution of the structure described here suggests a mechanism for the virion assembly and potentially provides a platform for the rational design of antiviral compounds and for the use of PVX in nanotechnology.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 22, 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 1.4Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
R: polyU RNA


Theoretical massNumber of molelcules
Total (without water)313,83414
Polymers313,83414
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area80080 Å2
ΔGint-584 kcal/mol
Surface area111830 Å2
MethodPISA

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Components

#1: Protein
Coat protein


Mass: 22519.514 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Potato virus X / References: UniProt: Q71E38, UniProt: P17782*PLUS
#2: RNA chain polyU RNA


Mass: 21080.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Potato virus X
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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

ComponentName: Potato virus X / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Potato virus X
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7
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: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
11RELION3classification
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 40.5 ° / Axial rise/subunit: 3.96 Å / Axial symmetry: C1
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 331130 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00622551
ELECTRON MICROSCOPYf_angle_d0.83531033
ELECTRON MICROSCOPYf_dihedral_angle_d14.96613487
ELECTRON MICROSCOPYf_chiral_restr0.0543595
ELECTRON MICROSCOPYf_plane_restr0.0063826

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