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Yorodumi- PDB-6rtk: CryoEM structure of modified Turnip Yellows Virus devoid of minor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rtk | ||||||
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Title | CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain | ||||||
Components | Major capsid protein | ||||||
Keywords | VIRUS | ||||||
Function / homology | Luteovirus group 1 coat protein / Luteovirus coat protein / T=3 icosahedral viral capsid / structural molecule activity / Major capsid protein Function and homology information | ||||||
Biological species | Turnip yellows virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | ||||||
Authors | Trapani, S. / Lai Kee Him, J. / Hoh, F. / Brault, V. / Bron, P. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain Authors: Trapani, S. / Lai Kee Him, J. / Boissinot, S. / Reinbold, C. / Fallet, C. / Ancelin, A. / Lecorre, F. / Hoh, F. / Ziegler-Graff, V. / Brault, V. / Bron, P. | ||||||
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 | 6rtk.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rtk.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 6rtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/6rtk ftp://data.pdbj.org/pub/pdb/validation_reports/rt/6rtk | HTTPS FTP |
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-Related structure data
Related structure data | 10001MC 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: 22522.520 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Turnip yellows virus (isolate FL-1) / Strain: isolate FL-1 / References: UniProt: P09508 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Beet western yellows virus-FL1 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Beet western yellows virus-FL1 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Virus shell | Name: capsid / Triangulation number (T number): 3 |
Buffer solution | pH: 6 |
Buffer component | Conc.: 0.1 mol / L / Name: citrate |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3003 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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