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Yorodumi- PDB-8feh: CryoEM structure of bacteriophage Q-beta coat protein dimer with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8feh | ||||||
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Title | CryoEM structure of bacteriophage Q-beta coat protein dimer with AYGG linker | ||||||
Components | Minor capsid protein A1 fusion | ||||||
Keywords | VIRUS LIKE PARTICLE / coat protein / q-beta / fusion | ||||||
Function / homology | Read-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1 Function and homology information | ||||||
Biological species | Qubevirus durum | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||
Authors | Newton, T.P. / Zhao, L. / Finn, M.G. / Kopylov, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of bacteriophage Q-beta coat protein dimer with AYGG linker Authors: Newton, T.P. / Zhao, L. / Kopylov, M. / Finn, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8feh.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8feh.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 8feh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8feh_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8feh_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8feh_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 8feh_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/8feh ftp://data.pdbj.org/pub/pdb/validation_reports/fe/8feh | HTTPS FTP |
-Related structure data
Related structure data | 29027MC 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 28604.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Qubevirus durum / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE1 |
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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: Qubevirus durum / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Qubevirus durum |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 64.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3838 / Height: 3710 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1380 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT |