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- PDB-6mwc: CryoEM structure of chimeric Eastern Equine Encephalitis Virus wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mwc | |||||||||||||||
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Title | CryoEM structure of chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-5 antibody | |||||||||||||||
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![]() | VIRUS/IMMUNE SYSTEM / Alphavirus / EEEV / Eastern Equine Encephalitis Virus / Sindbis / Fab / VIRUS-IMMUNE SYSTEM complex | |||||||||||||||
Function / homology | ![]() 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 / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||||||||
![]() | 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 | ![]() ![]()
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![]() | ![]() 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. | |||||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 877.9 KB | Display | ![]() |
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PDB format | ![]() | 721.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 160.9 KB | Display | |
Data in CIF | ![]() | 236.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9275MC ![]() 9249C ![]() 9274C ![]() 9278C ![]() 9279C ![]() 9280C ![]() 9281C ![]() 6muiC ![]() 6mw9C ![]() 6mwvC ![]() 6mwxC ![]() 6mx4C ![]() 6mx7C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 47938.141 Da / Num. of mol.: 4 / Fragment: ectodomain (UNP residues 802-1242) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 47046.953 Da / Num. of mol.: 4 / Fragment: ectodomain (UNP residues 325-744) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 23743.719 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Antibody | Mass: 23177.713 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) ![]() ![]() Sequence details | The antibody heavy chain and light chain amino acid sequences in this model are Fab CHK265 (from ...The antibody heavy chain and light chain amino acid sequences in this model are Fab CHK265 (from PDB entry 5ANY) and do not correspond to the amino acid sequences of the antibody heavy chain and light chains present in the sample. | |
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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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||
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 |
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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 |
Image recording | Electron dose: 31 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6583 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |