+Open data
-Basic information
Entry | Database: PDB / ID: 9jjg | |||||||||||||||
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Title | Cryo-EM structure of RHDV GI.2 virion | |||||||||||||||
Components | Genome polyprotein | |||||||||||||||
Keywords | VIRUS / Calicivirus / viral assembly / rabbit hemorrhagic disease virus (RHDV) / major capsid protein | |||||||||||||||
Function / homology | Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein Function and homology information | |||||||||||||||
Biological species | Rabbit hemorrhagic disease virus 2 | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||||||||
Authors | Ruan, Z. / Shao, Q. / Song, Y. / Hu, B. / Fan, Z. / Wei, H. / Liu, Y. / Wang, F. / Fang, Q. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: J.Virol. / Year: 2014 Title: Near-atomic structures of RHDV reveal insights into capsid assembly and different conformations between mature virion and VLP Authors: Ruan, Z. / Shao, Q. / Song, Y. / Hu, B. / Fan, Z. / Wei, H. / Liu, Y. / Wang, F. / Fang, Q. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9jjg.cif.gz | 264.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9jjg.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 9jjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9jjg_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9jjg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9jjg_validation.xml.gz | 63.9 KB | Display | |
Data in CIF | 9jjg_validation.cif.gz | 96.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/9jjg ftp://data.pdbj.org/pub/pdb/validation_reports/jj/9jjg | HTTPS FTP |
-Related structure data
Related structure data | 61526MC 9jjhC 9jjiC 9jjjC M: map data used to model this data C: citing same article (ref.) |
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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: 60419.926 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rabbit hemorrhagic disease virus 2 / Strain: GI.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A3S8Q1D6 Has protein modification | N | |
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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: Rabbit hemorrhagic disease virus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Rabbit hemorrhagic disease virus 2 |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: sf9 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Virus shell | Diameter: 410 nm / Triangulation number (T number): 3 |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
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 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.09 sec. / Electron dose: 26.09 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 270 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 33634 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21493 / Symmetry type: POINT |