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Yorodumi- EMDB-3020: The Molecular Basis for Flexibility in the Flexible Filamentous P... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3020 | |||||||||
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Title | The Molecular Basis for Flexibility in the Flexible Filamentous Plant Viruses | |||||||||
Map data | reconstruction of BaMV | |||||||||
Sample |
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Keywords | helical polymer / cumulative disorder / plant viruses | |||||||||
Function / homology | Potex/carlavirus coat protein / Viral coat protein / viral capsid / structural molecule activity / Coat protein Function and homology information | |||||||||
Biological species | Bamboo mosaic virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.6 Å | |||||||||
Authors | DiMaio F / Chen CC / Yu X / Frenz B / Hsu YH / Lin NS / Egelman EH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: The molecular basis for flexibility in the flexible filamentous plant viruses. Authors: Frank DiMaio / Chun-Chieh Chen / Xiong Yu / Brandon Frenz / Yau-Heiu Hsu / Na-Sheng Lin / Edward H Egelman / Abstract: Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have ...Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity. | |||||||||
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_3020.map.gz | 11.1 MB | EMDB map data format | |
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Header (meta data) | emd-3020-v30.xml emd-3020.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | EMD-3020-deposit.jpg | 81.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3020 | HTTPS FTP |
-Validation report
Summary document | emd_3020_validation.pdf.gz | 255.9 KB | Display | EMDB validaton report |
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Full document | emd_3020_full_validation.pdf.gz | 255 KB | Display | |
Data in XML | emd_3020_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3020 | HTTPS FTP |
-Related structure data
Related structure data | 5a2tMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3020.map.gz / Format: CCP4 / Size: 12.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of BaMV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : Bamboo mosaic virus
Entire | Name: Bamboo mosaic virus |
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Components |
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-Supramolecule #1000: Bamboo mosaic virus
Supramolecule | Name: Bamboo mosaic virus / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Bamboo mosaic virus
Supramolecule | Name: Bamboo mosaic virus / type: virus / ID: 1 / NCBI-ID: 35286 / Sci species name: Bamboo mosaic virus / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Chenopodium quinoa (quinoa) / synonym: PLANTAE(HIGHER PLANTS) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 1, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1474 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | IHRSR |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.0 Å Applied symmetry - Helical parameters - Δ&Phi: 40.9 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: OTHER / Software - Name: Spider |
CTF correction | Details: Each image |