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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 | ||||||
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Title | Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family | ||||||
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![]() | VIRUS / Coat Protein / RNA | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
![]() | Grinzato, A. / Kandiah, E. / Lico, C. / Betti, C. / Baschieri, S. / Zanotti, G. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 461.9 KB | Display | ![]() |
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PDB format | ![]() | 389.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 65.1 KB | Display | |
Data in CIF | ![]() | 93.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4740MC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 6.6 TB Data #1: Unaligned multi frame micographs of Potato Virus X dataset [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 22519.514 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() #2: RNA chain | | Mass: 21080.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Potato virus X / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 3 / Category: classification | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 40.5 ° / Axial rise/subunit: 3.96 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 331130 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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