+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26064 | |||||||||
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Title | SARS-CoV-2 S + Fabs 5317-4 and 5217-10 | |||||||||
Map data | SARS-CoV-2 S HexaPro bound to Fabs 5317-4 and 5317-10 | |||||||||
Sample |
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Keywords | neutralizing antibody / Fab / 5317 / viral immunity complex / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.64 Å | |||||||||
Authors | Johnson NV / McLellan JS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Biotechnol / Year: 2022 Title: Efficient discovery of SARS-CoV-2-neutralizing antibodies via B cell receptor sequencing and ligand blocking. Authors: Andrea R Shiakolas / Kevin J Kramer / Nicole V Johnson / Steven C Wall / Naveenchandra Suryadevara / Daniel Wrapp / Sivakumar Periasamy / Kelsey A Pilewski / Nagarajan Raju / Rachel Nargi / ...Authors: Andrea R Shiakolas / Kevin J Kramer / Nicole V Johnson / Steven C Wall / Naveenchandra Suryadevara / Daniel Wrapp / Sivakumar Periasamy / Kelsey A Pilewski / Nagarajan Raju / Rachel Nargi / Rachel E Sutton / Lauren M Walker / Ian Setliff / James E Crowe / Alexander Bukreyev / Robert H Carnahan / Jason S McLellan / Ivelin S Georgiev / Abstract: Although several monoclonal antibodies (mAbs) targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been approved for coronavirus disease 2019 (COVID-19) therapy, development ...Although several monoclonal antibodies (mAbs) targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been approved for coronavirus disease 2019 (COVID-19) therapy, development was generally inefficient, with lead generation often requiring the production and testing of numerous antibody candidates. Here, we report that the integration of target-ligand blocking with a previously described B cell receptor-sequencing approach (linking B cell receptor to antigen specificity through sequencing (LIBRA-seq)) enables the rapid and efficient identification of multiple neutralizing mAbs that prevent the binding of SARS-CoV-2 spike (S) protein to angiotensin-converting enzyme 2 (ACE2). The combination of target-ligand blocking and high-throughput antibody sequencing promises to increase the throughput of programs aimed at discovering new neutralizing antibodies. | |||||||||
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_26064.map.gz | 150.1 MB | EMDB map data format | |
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Header (meta data) | emd-26064-v30.xml emd-26064.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26064_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_26064.png | 47.1 KB | ||
Filedesc metadata | emd-26064.cif.gz | 4.4 KB | ||
Others | emd_26064_half_map_1.map.gz emd_26064_half_map_2.map.gz | 285.6 MB 285.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26064 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26064 | HTTPS FTP |
-Validation report
Summary document | emd_26064_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_26064_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_26064_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | emd_26064_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26064 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26064 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26064.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 S HexaPro bound to Fabs 5317-4 and 5317-10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map a
File | emd_26064_half_map_1.map | ||||||||||||
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Annotation | half map a | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map b
File | emd_26064_half_map_2.map | ||||||||||||
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Annotation | half map b | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of SARS-CoV-2 S-ECD with Fabs 5317-4 and 5317-10
Entire | Name: Complex of SARS-CoV-2 S-ECD with Fabs 5317-4 and 5317-10 |
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Components |
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-Supramolecule #1: Complex of SARS-CoV-2 S-ECD with Fabs 5317-4 and 5317-10
Supramolecule | Name: Complex of SARS-CoV-2 S-ECD with Fabs 5317-4 and 5317-10 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 240 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: -4 force, 3 s blot. | |||||||||
Details | Sample was monodisperse. S proteins had mixed occupancy of Fabs. Final reconstruction had 5 total Fabs bound: 3 5317-4 and 2 5317-10. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 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: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |