[English] 日本語
Yorodumi- PDB-6mx7: CryoEM structure of chimeric Eastern Equine Encephalitis Virus: G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mx7 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of chimeric Eastern Equine Encephalitis Virus: Genome-Binding Capsid N-terminal Domain | |||||||||||||||
Components | Capsid | |||||||||||||||
Keywords | VIRUS / Alphavirus / EEEV / Eastern Equine Encephalitis Virus / Sindbis | |||||||||||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / 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 ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / 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 | Eastern equine encephalitis virus | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||||||||
Authors | Hasan, S.S. / Sun, C. / Kim, A.S. / Watanabe, Y. / Chen, C.L. / Klose, T. / Buda, G. / Crispin, M. / Diamond, M.S. / Klimstra, W.B. / Rossmann, M.G. | |||||||||||||||
Funding support | United States, United Kingdom, 4items
| |||||||||||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Authors: S Saif Hasan / Chengqun Sun / Arthur S Kim / Yasunori Watanabe / Chun-Liang Chen / Thomas Klose / Geeta Buda / Max Crispin / Michael S Diamond / William B Klimstra / Michael G Rossmann / Abstract: Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an ...Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6mx7.cif.gz | 135.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6mx7.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mx7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6mx7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6mx7_validation.xml.gz | 49 KB | Display | |
Data in CIF | 6mx7_validation.cif.gz | 70.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/6mx7 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/6mx7 | HTTPS FTP |
-Related structure data
Related structure data | 9281MC 9249C 9274C 9275C 9278C 9279C 9280C 6muiC 6mw9C 6mwcC 6mwvC 6mwxC 6mx4C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 28861.496 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 1-260) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Cell (production host): BHK-15 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P27284 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Eastern equine encephalitis virus capsid / Type: COMPLEX / Details: Purified from infected BHK-15 cells / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Eastern equine encephalitis virus |
Source (recombinant) | Organism: Mesocricetus auratus (golden hamster) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: HELIUM / Humidity: 80 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 |
Image recording | Electron dose: 31 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30806 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |