+Open data
-Basic information
Entry | Database: PDB / ID: 9fhp | ||||||
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Title | CryoEM structure of wild-type Turnip Yellows Virus | ||||||
Components | Minor capsid readthrough protein | ||||||
Keywords | VIRUS / read-through protein | ||||||
Function / homology | Potato leaf roll virus readthrough protein / Potato leaf roll virus readthrough protein / Luteovirus group 1 coat protein / Luteovirus coat protein / host cell plasmodesma / host cell periplasmic space / viral capsid / structural molecule activity / Readthrough protein P3-RTD Function and homology information | ||||||
Biological species | Turnip yellows virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 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 wild-type Turnip Yellows Virus Authors: Lai Kee Him, J. / Trapani, S. / Boissinot, S. / Reinold, C. / Fallet, C. / Ancelin, A. / Lecorre, F. / Hoh, F. / Ziegler-Graff, V. / Brault, V. / Bron, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fhp.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fhp.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 9fhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fhp_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9fhp_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9fhp_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 9fhp_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/9fhp ftp://data.pdbj.org/pub/pdb/validation_reports/fh/9fhp | HTTPS FTP |
-Related structure data
Related structure data | M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 genetically manipulated source Source: (gene. exp.) Turnip yellows virus / Gene: ORF3/ORF5 / Production host: Nicotiana benthamiana (plant) / References: UniProt: P09514 |
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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: Turnip yellows virus / Type: VIRUS / Details: agroiniltration (English et al. 1997) / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Turnip yellows virus |
Source (recombinant) | Organism: Nicotiana benthamiana (plant) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Buffer solution | pH: 6 |
Buffer component | Conc.: 0.1 mol/L / Name: citrate |
Specimen | Conc.: 1.32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||
3D reconstruction | Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17316 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||
Atomic model building | PDB-ID: 6rtk Accession code: 6rtk / Source name: PDB / Type: experimental model |