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Yorodumi- PDB-5a2t: The Molecular Basis for Flexibility in the Flexible Filamentous P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a2t | ||||||
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Title | The Molecular Basis for Flexibility in the Flexible Filamentous Plant Viruses | ||||||
Components |
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Keywords | VIRAL PROTEIN / HELICAL POLYMER / CUMULATIVE DISORDER / PLANT VIRUSES | ||||||
Function / homology | Potex/carlavirus coat protein / Viral coat protein / viral capsid / structural molecule activity / RNA / RNA (> 10) / RNA (> 100) / Coat protein Function and homology information | ||||||
Biological species | BAMBOO MOSAIC VIRUS | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.6 Å | ||||||
Authors | DiMaio, F. / Chen, C.C. / Yu, X. / Frenz, B. / Hsu, Y.H. / Lin, N.S. / Egelman, E.H. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5a2t.cif.gz | 978.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a2t.ent.gz | 836.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a2t ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a2t | HTTPS FTP |
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-Related structure data
Related structure data | 3020MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 22351.225 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) BAMBOO MOSAIC VIRUS / References: UniProt: O37178 #2: RNA chain | | Mass: 38225.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BAMBOO MOSAIC VIRUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: BAMV / Type: VIRUS |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Nov 1, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Details: IMAGES | ||||||||||||
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3D reconstruction | Method: IHRSR / Resolution: 5.6 Å / Num. of particles: 104433 / Nominal pixel size: 1.05 Å / Actual pixel size: 1.05 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3020. (DEPOSITION ID: 13412). Symmetry type: HELICAL | ||||||||||||
Refinement | Highest resolution: 5.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5.6 Å
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