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Yorodumi- EMDB-4740: Atomic structure of potato virus X, the prototype of the Alphafle... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4740 | |||||||||
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Title | Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Virus / Coat Protein / RNA | |||||||||
Function / homology | Potexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / helical viral capsid / viral capsid / structural molecule activity / Coat protein / Coat protein Function and homology information | |||||||||
Biological species | Potato virus X | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Grinzato A / Kandiah E | |||||||||
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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4740.map.gz | 166.4 MB | EMDB map data format | |
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Header (meta data) | emd-4740-v30.xml emd-4740.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_4740.png | 58.9 KB | ||
Filedesc metadata | emd-4740.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4740 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4740 | HTTPS FTP |
-Validation report
Summary document | emd_4740_validation.pdf.gz | 630.6 KB | Display | EMDB validaton report |
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Full document | emd_4740_full_validation.pdf.gz | 630.2 KB | Display | |
Data in XML | emd_4740_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_4740_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4740 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4740 | HTTPS FTP |
-Related structure data
Related structure data | 6r7gMC M: atomic model generated by this map C: citing same article (ref.) |
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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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4740.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Potato virus X
Entire | Name: Potato virus X |
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Components |
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-Supramolecule #1: Potato virus X
Supramolecule | Name: Potato virus X / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 12183 / Sci species name: Potato virus X / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Potato virus X |
Molecular weight | Theoretical: 22.519514 KDa |
Sequence | String: ASGLFTIPDG DFFSTARAIV ASNAVATNED LSKIEAIWKD MKVPTDTMAQ AAWDLVRHCA DVGSSAQTEM IDTGPYSNGI SRARLAAAI KEVCTLRQFC MKYAPVVWNW MLTNNSPPAN WQAQGFKPEH KFAAFDFFNG VTNPAAIMPK EGLIRPPSEA E MNAAQTAA ...String: ASGLFTIPDG DFFSTARAIV ASNAVATNED LSKIEAIWKD MKVPTDTMAQ AAWDLVRHCA DVGSSAQTEM IDTGPYSNGI SRARLAAAI KEVCTLRQFC MKYAPVVWNW MLTNNSPPAN WQAQGFKPEH KFAAFDFFNG VTNPAAIMPK EGLIRPPSEA E MNAAQTAA FVKITKARAQ SNDFASLDAA VTRGRITGTT TAEAVVTLPP P UniProtKB: Coat protein |
-Macromolecule #2: polyU RNA
Macromolecule | Name: polyU RNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Potato virus X |
Molecular weight | Theoretical: 21.080488 KDa |
Sequence | String: UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 92 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 3.96 Å Applied symmetry - Helical parameters - Δ&Phi: 40.5 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 331130 |
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Startup model | Type of model: INSILICO MODEL |
Final angle assignment | Type: NOT APPLICABLE |