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Yorodumi- PDB-7xgz: Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xgz | ||||||
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Title | Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid at pH 7.5 | ||||||
Components | Capsid protein alpha | ||||||
Keywords | VIRUS LIKE PARTICLE | ||||||
Function / homology | Viral coat protein subunit / Capsid protein alpha Function and homology information | ||||||
Biological species | Lake Sinai virus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å | ||||||
Authors | Chen, N.C. / Wang, C.H. / Chen, C.J. / Yoshimura, M. / Guan, H.H. / Chuankhayan, P. / Lin, C.C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions Authors: Chen, N.C. / Wang, C.H. / Yoshimura, M. / Yeh, Y.Q. / Guan, H.H. / Chuankhayan, P. / Lin, C.C. / Lin, P.J. / Huang, Y.C. / Wakatsuki, S. / Ho, M.C. / Chen, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xgz.cif.gz | 309.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xgz.ent.gz | 254.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/7xgz ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xgz | HTTPS FTP |
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-Related structure data
Related structure data | 33190MC 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 57344.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lake Sinai virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEV4 |
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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: Lake Sinai virus 2 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Lake Sinai virus 2 |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 defocus max: 2720 nm / Nominal defocus min: 250 nm |
Image recording | Electron dose: 46 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||
Particle selection | Num. of particles selected: 30227 | |||||||||||||||
3D reconstruction | Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30227 / Symmetry type: POINT |