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Yorodumi- EMDB-28116: Western Equine Encephalitis Virus-Like Particle in Complex with S... -
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-Basic information
Entry | Database: EMDB / ID: EMD-28116 | |||||||||
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Title | Western Equine Encephalitis Virus-Like Particle in Complex with SKW24 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Western Equine Encephalitis Virus / virus like particle / antibody / VLP-Fab complex | |||||||||
Biological species | Homo sapiens (human) / Western equine encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Pletnev S / Tsybovsky Y / Verardi R / Roedeger M / Kwong PD | |||||||||
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_28116.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-28116-v30.xml emd-28116.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_28116.png | 111.2 KB | ||
Filedesc metadata | emd-28116.cif.gz | 4.2 KB | ||
Others | emd_28116_half_map_1.map.gz emd_28116_half_map_2.map.gz | 1.8 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28116 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28116 | 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_28116.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28116_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28116_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Western Equine Encephalitis Virus-Like Particle in Complex with S...
Entire | Name: Western Equine Encephalitis Virus-Like Particle in Complex with SKW24 Fab |
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Components |
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-Supramolecule #1: Western Equine Encephalitis Virus-Like Particle in Complex with S...
Supramolecule | Name: Western Equine Encephalitis Virus-Like Particle in Complex with SKW24 Fab type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #3: SKW24 Fab
Supramolecule | Name: SKW24 Fab / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Western equine encephalitis virus
Supramolecule | Name: Western equine encephalitis virus / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 5220 / Average electron dose: 46.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 55490 / Details: VLPs |
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Startup model | Type of model: INSILICO MODEL |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 33238 |
-Atomic model buiding 1
Refinement | Space: REAL |
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