[English] 日本語
Yorodumi- PDB-6r7g: Atomic structure of potato virus X, the prototype of the Alphafle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r7g | ||||||
---|---|---|---|---|---|---|---|
Title | Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family | ||||||
Components |
| ||||||
Keywords | VIRUS / Coat Protein / RNA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Potato virus X | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
Authors | Grinzato, A. / Kandiah, E. / Lico, C. / Betti, C. / Baschieri, S. / Zanotti, G. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6r7g.cif.gz | 461.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6r7g.ent.gz | 389.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r7g_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6r7g_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6r7g_validation.xml.gz | 65.1 KB | Display | |
Data in CIF | 6r7g_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/6r7g ftp://data.pdbj.org/pub/pdb/validation_reports/r7/6r7g | HTTPS FTP |
-Related structure data
Related structure data | 4740MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10705 (Title: structure of potato virus X, the prototype of the Alphaflexiviridae family Data size: 6.6 TB Data #1: Unaligned multi frame micographs of Potato Virus X dataset [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: 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 | | Mass: 21080.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Potato virus X #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Potato virus X / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
---|---|
Source (natural) | Organism: Potato virus X |
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|