+Open data
-Basic information
Entry | Database: PDB / ID: 7wc2 | ||||||
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Title | Cryo-EM structure of alphavirus, Getah virus | ||||||
Components |
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Keywords | VIRUS / alphavirus / Getah virus / Togaviridae / structural genomics | ||||||
Function / homology | Function and homology information 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 | Getah virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Wang, M. / Sun, Z.Z. / Wang, J.F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wc2.cif.gz | 600.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wc2.ent.gz | 497.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wc2_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7wc2_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7wc2_validation.xml.gz | 93.5 KB | Display | |
Data in CIF | 7wc2_validation.cif.gz | 142.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/7wc2 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/7wc2 | HTTPS FTP |
-Related structure data
Related structure data | 32412MC 7vgaC 7wcoC 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
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 47620.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Getah virus / References: UniProt: Q5Y388 #2: Protein | Mass: 46416.793 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Getah virus / References: UniProt: Q5Y388 #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Has ligand of interest | N | Has protein modification | 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 |
-Sample preparation
Component | Name: Getah virus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Getah virus |
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 |
-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: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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Particle selection | Num. of particles selected: 36066 / Details: region for particle picking |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30996 / Symmetry type: POINT |