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Yorodumi- EMDB-28187: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28187 | |||||||||
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Title | Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP | |||||||||
Map data | VLP I1 map | |||||||||
Sample |
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Keywords | antibody / alphavirus / VEEV / spike / glycoprotein / VIRAL PROTEIN | |||||||||
Biological species | Venezuelan equine encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Casner RG / Verardi R / Roederer M / Shapiro L | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2023 Title: Vaccine elicitation and structural basis for antibody protection against alphaviruses. Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / ...Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / Raffaello Verardi / Baoshan Zhang / David Ambrozak / Margaret Beddall / Hong Lei / Eun Sung Yang / Tracy Liu / Amy R Henry / Reda Rawi / Arne Schön / Chaim A Schramm / Chen-Hsiang Shen / Wei Shi / Tyler Stephens / Yongping Yang / Maria Burgos Florez / Julie E Ledgerwood / Crystal W Burke / Lawrence Shapiro / Julie M Fox / Peter D Kwong / Mario Roederer / Abstract: Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine ...Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28187.map.gz | 271.7 MB | EMDB map data format | |
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Header (meta data) | emd-28187-v30.xml emd-28187.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28187_fsc.xml | 20.3 KB | Display | FSC data file |
Images | emd_28187.png | 132.9 KB | ||
Others | emd_28187_half_map_1.map.gz emd_28187_half_map_2.map.gz | 273.4 MB 272.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28187 | HTTPS FTP |
-Validation report
Summary document | emd_28187_validation.pdf.gz | 644.9 KB | Display | EMDB validaton report |
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Full document | emd_28187_full_validation.pdf.gz | 644.4 KB | Display | |
Data in XML | emd_28187_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | emd_28187_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28187 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28187 | HTTPS FTP |
-Related structure data
Related structure data | 8decC 8dedC 8deeC 8defC 8deqC 8derC 8dulC 8dunC 8dwoC 8eeuC 8eevC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28187.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | VLP I1 map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.32 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: VLP I1 half map 1
File | emd_28187_half_map_1.map | ||||||||||||
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Annotation | VLP I1 half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: VLP I1 half map 2
File | emd_28187_half_map_2.map | ||||||||||||
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Annotation | VLP I1 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV ...
Entire | Name: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP |
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Components |
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-Supramolecule #1: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV ...
Supramolecule | Name: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Venezuelan equine encephalitis virus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |