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Yorodumi- EMDB-3144: Electron cryo-microscopy of chikungunya virus in complex with neu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3144 | |||||||||
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Title | Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab CHK265 | |||||||||
Map data | Reconstruction of chikungunya virus in complex with Fab | |||||||||
Sample |
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Keywords | chikungunya virus / neutralizing antibody Fab | |||||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Chikungunya virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.9 Å | |||||||||
Authors | Fox JM / Long F / Edeling MA / Lin H / Duijl-Richter M / Fong RH / Kahle KM / Smit JM / Jin J / Simmons G ...Fox JM / Long F / Edeling MA / Lin H / Duijl-Richter M / Fong RH / Kahle KM / Smit JM / Jin J / Simmons G / Doranz BJ / Crowe JE / Fremont DH / Rossmann MG / Diamond MS | |||||||||
Citation | Journal: Cell / Year: 2015 Title: Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress. Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / ...Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / James E Crowe / Daved H Fremont / Michael G Rossmann / Michael S Diamond / Abstract: We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of ...We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O'nyong'nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3144.map.gz | 99.6 MB | EMDB map data format | |
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Header (meta data) | emd-3144-v30.xml emd-3144.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd-3144-CHIKV_CHK265_500by500.tif | 1.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3144 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3144 | HTTPS FTP |
-Validation report
Summary document | emd_3144_validation.pdf.gz | 263.3 KB | Display | EMDB validaton report |
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Full document | emd_3144_full_validation.pdf.gz | 262.4 KB | Display | |
Data in XML | emd_3144_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3144 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3144 | HTTPS FTP |
-Related structure data
Related structure data | 5anyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3144.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of chikungunya virus in complex with Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Electron Cryo-microscopy of Chikungunya virus 181/25 in complex w...
Entire | Name: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex with murine neutralizing antibody Fab CHK265 |
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Components |
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-Supramolecule #1000: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex w...
Supramolecule | Name: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex with murine neutralizing antibody Fab CHK265 type: sample / ID: 1000 Oligomeric state: one Fab binds to one envelope protein on the surface of virus Number unique components: 2 |
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-Supramolecule #1: Chikungunya virus
Supramolecule | Name: Chikungunya virus / type: virus / ID: 1 / Name.synonym: Chikungunya virus strain TSI-GSD-218 / NCBI-ID: 37124 / Sci species name: Chikungunya virus Sci species strain: strain TSI-GSD-218 or vaccine strain 181/25 Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Chikungunya virus strain TSI-GSD-218 |
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Host (natural) | Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES |
Host system | Organism: Chlorocebus aethiops (grivet) / Recombinant cell: Vero cells |
Virus shell | Shell ID: 1 / Diameter: 700 Å / T number (triangulation number): 4 |
-Macromolecule #1: Fab CHK265
Macromolecule | Name: Fab CHK265 / type: protein_or_peptide / ID: 1 / Number of copies: 240 / Recombinant expression: No |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: Mouse / Cell: hybridoma |
Molecular weight | Experimental: 50 KDa / Theoretical: 50 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.2 / Details: PBS |
Grid | Details: 400 mesh ultrathin holey carbon copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 110 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 10 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Mar 10, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 500 / Average electron dose: 22 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 78354 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were mannually selected using the program EMAN2. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.9 Å / Resolution method: OTHER / Software - Name: JSPR / Number images used: 5828 |