+Open data
-Basic information
Entry | Database: PDB / ID: 8r0f | ||||||||||||
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Title | Capsid structure of Giardiavirus (GLV) HP strain | ||||||||||||
Components | Capsid protein | ||||||||||||
Keywords | VIRUS / Giardia parasite / dsRNA virus / capsid structure / cryo / Totiviridae / Giardia lambia virus (GLV) | ||||||||||||
Function / homology | Capsid protein Function and homology information | ||||||||||||
Biological species | Giardia lamblia virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å | ||||||||||||
Authors | Wang, H. / Gianluca, M. / Munke, A. / Hassan, M.M. / Lalle, M. / Okamoto, K. | ||||||||||||
Funding support | Sweden, Norway, 3items
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Citation | Journal: To Be Published Title: Capsid structure of Giardiavirus (GLV) HP strain Authors: Wang, H. / Gianluca, M. / Munke, A. / Hassan, M.M. / Lalle, M. / Okamoto, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r0f.cif.gz | 322.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r0f.ent.gz | 259.5 KB | Display | PDB format |
PDBx/mmJSON format | 8r0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r0f_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8r0f_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8r0f_validation.xml.gz | 60.2 KB | Display | |
Data in CIF | 8r0f_validation.cif.gz | 88.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/8r0f ftp://data.pdbj.org/pub/pdb/validation_reports/r0/8r0f | HTTPS FTP |
-Related structure data
Related structure data | 18791MC 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: 103481.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia virus / References: UniProt: A0A8F6AHR5 |
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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: Giardia lamblia virus / Type: VIRUS Details: GLV isolated from Giardia duodenalis isolates HP-1 from a human patient. Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Giardia lamblia virus / Strain: HP-1 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Giardia intestinalis / Strain: HP-1 |
Virus shell | Name: Capsid / Diameter: 450 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 7.4 / Details: 1 x PBS (-) |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified GLV-HP particles |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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 / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28342 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6S2C Accession code: 6S2C / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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