+Open data
-Basic information
Entry | Database: PDB / ID: 7ncr | ||||||
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Title | Cryo-EM structure of Pepper cryptic virus 1 VLP | ||||||
Components | Coat protein | ||||||
Keywords | VIRUS LIKE PARTICLE / Partitivirus / Capsid | ||||||
Function / homology | viral capsid / membrane => GO:0016020 / Coat protein Function and homology information | ||||||
Biological species | Pepper cryptic virus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Byrne, M.J. / Sainsbury, F. / Ranson, N.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure of Pepper Cryptic Virus 1 VLP Authors: Byrne, M.J. / Sainsbury, F. / Ranson, N.A. / Kashyap, A. / Esquirol, L. | ||||||
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 | 7ncr.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ncr.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ncr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/7ncr ftp://data.pdbj.org/pub/pdb/validation_reports/nc/7ncr | HTTPS FTP |
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-Related structure data
Related structure data | 12270MC 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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-Components
#1: Protein | Mass: 47626.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pepper cryptic virus 1 / Production host: Nicotiana benthamiana (plant) / References: UniProt: F8VBM8 |
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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: Pepper cryptic virus 1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Pepper cryptic virus 1 |
Source (recombinant) | Organism: Nicotiana benthamiana (plant) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7 Details: 20 mM MOPS, pH 7.0 with 140 mM NaCl and 5% (v/v) glycerol |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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: 1.12 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90000 / Symmetry type: POINT | ||||||||||||||||||||||||
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