+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41076 | |||||||||
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Title | SARS-CoV-2 spike in complex with Fab 71281-33 (2) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | viral-protein / fab / IMMUNE complex / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Binshtein E / Crowe JE | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep Med / Year: 2023 Title: SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes. Authors: Steven C Wall / Naveenchandra Suryadevara / Changil Kim / Andrea R Shiakolas / Clinton M Holt / Emma B Irbe / Perry T Wasdin / Yukthi P Suresh / Elad Binshtein / Elaine C Chen / Seth J Zost ...Authors: Steven C Wall / Naveenchandra Suryadevara / Changil Kim / Andrea R Shiakolas / Clinton M Holt / Emma B Irbe / Perry T Wasdin / Yukthi P Suresh / Elad Binshtein / Elaine C Chen / Seth J Zost / Elizabeth Canfield / James E Crowe / Mary Ann Thompson-Arildsen / Daniel J Sheward / Robert H Carnahan / Ivelin S Georgiev / Abstract: From the beginning of the COVID-19 pandemic, children have exhibited different susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, reinfection, and disease ...From the beginning of the COVID-19 pandemic, children have exhibited different susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, reinfection, and disease compared with adults. Motivated by the established significance of SARS-CoV-2-neutralizing antibodies in adults, here we characterize SARS-CoV-2-specific antibody repertoires in a young cohort of individuals aged from 5 months to 18 years old. Our results show that neutralizing antibodies in children possess similar genetic features compared to antibodies identified in adults, with multiple antibodies from children belonging to previously established public antibody clonotypes in adults. Notably, antibodies from children show potent neutralization of circulating SARS-CoV-2 variants that have cumulatively resulted in resistance to virtually all approved monoclonal antibody therapeutics. Our results show that children can rely on similar SARS-CoV-2 antibody neutralization mechanisms compared to adults and are an underutilized source for the discovery of effective antibody therapeutics to counteract the ever-evolving pandemic. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41076.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-41076-v30.xml emd-41076.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_41076.png | 16.7 KB | ||
Filedesc metadata | emd-41076.cif.gz | 4.2 KB | ||
Others | emd_41076_half_map_1.map.gz emd_41076_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41076 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41076 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41076.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 4.36 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41076_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41076_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cov2 spike in complex with Fab 71281-33
Entire | Name: Cov2 spike in complex with Fab 71281-33 |
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Components |
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-Supramolecule #1: Cov2 spike in complex with Fab 71281-33
Supramolecule | Name: Cov2 spike in complex with Fab 71281-33 / type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: Cov2-spike
Supramolecule | Name: Cov2-spike / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Fab
Supramolecule | Name: Fab / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 8 |
Staining | Type: NEGATIVE / Material: uranyl formate |
Grid | Support film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 247 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final 3D classification | Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5408 |
-Atomic model buiding 1
Refinement | Space: REAL |
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