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Yorodumi- EMDB-1437: Sindbis virus conformational changes induced by a neutralizing an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1437 | |||||||||
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Title | Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody. | |||||||||
Map data | angel | |||||||||
Sample |
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Biological species | unidentified (others) / Sindbis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 24.0 Å | |||||||||
Authors | Paredes AM / Hernandez R / West M / Brown DT | |||||||||
Citation | Journal: J Virol / Year: 2008 Title: Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody. Authors: Raquel Hernandez / Angel Paredes / Dennis T Brown / Abstract: A rare Sindbis virus anti-E1 neutralizing monoclonal antibody, Sin-33, was investigated to determine the mechanism of in vitro neutralization. A cryoelectron microscopic reconstruction of Sindbis ...A rare Sindbis virus anti-E1 neutralizing monoclonal antibody, Sin-33, was investigated to determine the mechanism of in vitro neutralization. A cryoelectron microscopic reconstruction of Sindbis virus (SVHR) neutralized with FAb from Sin-33 (FAb-33) revealed conformational changes on the surface of the virion at a resolution of 24 A. FAb-33 was found to bind E1 in less than 1:1 molar ratios, as shown by the absence of FAb density in the reconstruction and stoichiometric measurements using radiolabeled FAb-33, which determined that about 60 molecules of FAb-33 bound to the 240 possible sites in a single virus particle. FAb-33-neutralized virus particles became sensitive to digestion by endoproteinase Glu-C, providing further evidence of antibody-induced structural changes within the virus particle. The treatment of FAb-33-neutralized or Sin-33-neutralized SVHR with low pH did not induce the conformational rearrangements required for virus membrane-cell membrane fusion. Exposure to low pH, however, increased the amount of Sin-33 or FAb-33 that bound to the virus particles, indicating the exposure of additional epitopes. The neutralization of SVHR infection by FAb-33 or Sin-33 did not prevent the association of virus with host cells. These data are in agreement with the results of previous studies that demonstrated that specific antibodies can inactivate the infectious state of a metastable virus in vitro by the induction of conformational changes to produce an inactive structure. A model is proposed which postulates that the induction of conformational changes in the infectious state of a metastable enveloped virus may be a general mechanism of antibody inactivation of virus infectivity. | |||||||||
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_1437.map.gz | 21 MB | EMDB map data format | |
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Header (meta data) | emd-1437-v30.xml emd-1437.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | 1437.gif | 95.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1437 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1437 | HTTPS FTP |
-Validation report
Summary document | emd_1437_validation.pdf.gz | 254.4 KB | Display | EMDB validaton report |
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Full document | emd_1437_full_validation.pdf.gz | 253.5 KB | Display | |
Data in XML | emd_1437_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1437 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1437 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1437.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | angel | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 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 : Sin-33 Fab treated Sindbis virus
Entire | Name: Sin-33 Fab treated Sindbis virus |
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Components |
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-Supramolecule #1000: Sin-33 Fab treated Sindbis virus
Supramolecule | Name: Sin-33 Fab treated Sindbis virus / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Theoretical: 45 MDa / Method: STEM mass measurements Brookhaven, NY. |
-Supramolecule #1: Sindbis virus
Supramolecule | Name: Sindbis virus / type: virus / ID: 1 / NCBI-ID: 11034 / Sci species name: Sindbis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Culex (mosquito) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Name: Envelope / Diameter: 680 Å / T number (triangulation number): 4 |
Virus shell | Shell ID: 2 / Name: Nucleocapsid / Diameter: 400 Å / T number (triangulation number): 4 |
-Macromolecule #1: Fab
Macromolecule | Name: Fab / type: protein_or_peptide / ID: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 20 mM MOPS, 100 mM NaCl |
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Grid | Details: holey carbon film |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 110 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: Blot holey carbon grid from behind |
-Electron microscopy
Microscope | JEOL 4000EX |
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Temperature | Average: 110 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 16 µm / Number real images: 6 / Average electron dose: 5 e/Å2 |
Electron beam | Acceleration voltage: 400 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: CTF correction of each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: MRC Details: Final map was calculated from 19 class averages using EMAN and imposing icosahedral symmetry Number images used: 858 |
Final two d classification | Number classes: 19 |