[English] 日本語
Yorodumi- EMDB-28117: Eastern Equine Encephalitis Virus-Like Particle in Complex with S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28117 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Eastern Equine Encephalitis virus / Virus-Like Particle / virus-fab complex / VIRUS LIKE PARTICLE | |||||||||
Biological species | Macaca fascicularis (crab-eating macaque) / Eastern equine encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Pletnev S / Verardi R / Roedeger M / Kwong P | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28117.map.gz | 1.2 GB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28117-v30.xml emd-28117.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_28117.png | 112.1 KB | ||
Filedesc metadata | emd-28117.cif.gz | 4.4 KB | ||
Others | emd_28117_half_map_1.map.gz emd_28117_half_map_2.map.gz | 1.2 GB 1.2 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28117 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28117 | HTTPS FTP |
-Related structure data
Related structure data | 8decC 8dedC 8deeC 8defC 8deqC 8derC 8dulC 8dunC 8dwoC 8eeuC 8eevC C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_28117.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.66 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_28117_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_28117_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Eastern Equine Encephalitis Virus-Like Particle in Complex with S...
Entire | Name: Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab |
---|---|
Components |
|
-Supramolecule #1: Eastern Equine Encephalitis Virus-Like Particle in Complex with S...
Supramolecule | Name: Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab type: complex / ID: 1 / Parent: 0 |
---|
-Supramolecule #3: SKE26 Fab
Supramolecule | Name: SKE26 Fab / type: complex / ID: 3 / Parent: 1 |
---|---|
Source (natural) | Organism: Macaca fascicularis (crab-eating macaque) |
-Supramolecule #2: Eastern equine encephalitis virus
Supramolecule | Name: Eastern equine encephalitis virus / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
---|
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: 0.7000000000000001 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: 5662 / Average electron dose: 58.06 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 78534 |
---|---|
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3) |
Final 3D classification | Number classes: 7 / Avg.num./class: 8627 / 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 51190 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Refinement | Space: REAL |