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Open data
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Basic information
Entry | Database: PDB / ID: 7vga | ||||||
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Title | Cryo-EM structure of alphavirus, Getah virus | ||||||
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![]() | VIRUS / alphavirus / Getah virus / Togaviridae / structural genomics | ||||||
Function / homology | ![]() togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å | ||||||
![]() | Wang, M. / Sun, Z.Z. / Wang, J.F. | ||||||
Funding support | 1items
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![]() | ![]() Title: Implications for the pathogenicity and antigenicity of alpha viruses revealed by a 3.5 angstrom Cryo-EM structure of Getah virus Authors: Wang, M. / Sun, Z.Z. / Wang, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.4 KB | Display | ![]() |
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PDB format | ![]() | 148.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 992.5 KB | Display | ![]() |
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Full document | ![]() | 997.9 KB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 45.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31966MC ![]() 7wc2C ![]() 7wcoC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 47620.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 46416.793 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 30200.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: alphavirus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Getah virus |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING ONLY |
Particle selection | Num. of particles selected: 36066 / Details: region for particle picking |
3D reconstruction | Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30996 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Symmetry type: POINT |