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Yorodumi- EMDB-2645: Electron Cryo-microscopy of Venezuelan Equine Encephalitis Virus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2645 | |||||||||
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Title | Electron Cryo-microscopy of Venezuelan Equine Encephalitis Virus TC-83 in complex with neutralizing antibody Fab F5 | |||||||||
Map data | Reconstruction of VEEV TC-83 in complex with a Fab fragment from neutralizing antibody F5. | |||||||||
Sample |
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Keywords | Alphavirus / Venezuelan / antibody neutralization / Fab | |||||||||
Biological species | Mus musculus (house mouse) / Venezuelan equine encephalitis virus (strain TC-83) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Porta JC / Jose J / Roehrig JT / Blair CD / Kuhn RJ / Rossmann MG | |||||||||
Citation | Journal: J Virol / Year: 2014 Title: Locking and blocking the viral landscape of an alphavirus with neutralizing antibodies. Authors: Jason Porta / Joyce Jose / John T Roehrig / Carol D Blair / Richard J Kuhn / Michael G Rossmann / Abstract: Alphaviruses are serious, sometimes lethal human pathogens that belong to the family Togaviridae. The structures of human Venezuelan equine encephalitis virus (VEEV), an alphavirus, in complex with ...Alphaviruses are serious, sometimes lethal human pathogens that belong to the family Togaviridae. The structures of human Venezuelan equine encephalitis virus (VEEV), an alphavirus, in complex with two strongly neutralizing antibody Fab fragments (F5 and 3B4C-4) have been determined using a combination of cryo-electron microscopy and homology modeling. We characterize these monoclonal antibody Fab fragments, which are known to abrogate VEEV infectivity by binding to the E2 (envelope) surface glycoprotein. Both of these antibody Fab fragments cross-link the surface E2 glycoproteins and therefore probably inhibit infectivity by blocking the conformational changes that are required for making the virus fusogenic. The F5 Fab fragment cross-links E2 proteins within one trimeric spike, whereas the 3B4C-4 Fab fragment cross-links E2 proteins from neighboring spikes. Furthermore, F5 probably blocks the receptor-binding site, whereas 3B4C-4 sterically hinders the exposure of the fusion loop at the end of the E2 B-domain. IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Venezuelan equine encephalitis virus (VEEV) is an alphavirus with a wide distribution across the globe. No effective vaccines ...IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Venezuelan equine encephalitis virus (VEEV) is an alphavirus with a wide distribution across the globe. No effective vaccines exist for alphaviral infections. Therefore, a better understanding of VEEV and its associated neutralizing antibodies will help with the development of effective drugs and vaccines. | |||||||||
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_2645.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-2645-v30.xml emd-2645.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | EMD-2635_hMED.jpg | 63.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2645 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2645 | HTTPS FTP |
-Validation report
Summary document | emd_2645_validation.pdf.gz | 255.2 KB | Display | EMDB validaton report |
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Full document | emd_2645_full_validation.pdf.gz | 254.3 KB | Display | |
Data in XML | emd_2645_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2645 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2645 | HTTPS FTP |
-Related structure data
Related structure data | 4uomMC 2655C 4uokC 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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-Map
File | Download / File: emd_2645.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of VEEV TC-83 in complex with a Fab fragment from neutralizing antibody F5. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.28 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 : VEEV TC-83 in complex with Fab fragments of neutralizing antibody F5
Entire | Name: VEEV TC-83 in complex with Fab fragments of neutralizing antibody F5 |
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Components |
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-Supramolecule #1000: VEEV TC-83 in complex with Fab fragments of neutralizing antibody F5
Supramolecule | Name: VEEV TC-83 in complex with Fab fragments of neutralizing antibody F5 type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 5.25 MDa / Theoretical: 5.25 MDa / Method: UV-VIS |
-Supramolecule #1: Venezuelan equine encephalitis virus (strain TC-83)
Supramolecule | Name: Venezuelan equine encephalitis virus (strain TC-83) / type: virus / ID: 1 / Name.synonym: VEEV / NCBI-ID: 11037 Sci species name: Venezuelan equine encephalitis virus (strain TC-83) Sci species strain: Trinidad Donkey / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: VEEV |
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Host (natural) | Organism: Equus asinus (ass) / synonym: VERTEBRATES |
Host system | Organism: Mesocricetus auratus (golden hamster) / Recombinant cell: BHK-15 |
Molecular weight | Experimental: 5.25 MDa / Theoretical: 5.25 MDa |
Virus shell | Shell ID: 1 / Name: E1E2 / Diameter: 700 Å / T number (triangulation number): 4 |
-Macromolecule #1: Fab fragments of neutralizing antibody F5
Macromolecule | Name: Fab fragments of neutralizing antibody F5 / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.6 / Details: 50 mM TRIS-HCl, 100 mM NaCl, 0.1 M EDTA |
Grid | Details: 200 mesh Cu Quantifoil grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 130 K / Instrument: HOMEMADE PLUNGER / Details: Grids prepared under BSL-2 hood / Method: Blot for 5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100 K / Max: 105 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification |
Specialist optics | Energy filter - Name: FEI / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 50.0 eV |
Date | Jul 14, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 112 / Average electron dose: 24 e/Å2 / Od range: 1.5 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 60521 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
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 selected manually using the EMAN2 boxing program |
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CTF correction | Details: Each particle/image |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: EMAN1/2 / Number images used: 1389 |
Final two d classification | Number classes: 10 |