+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25073 | |||||||||
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Title | Structure of Fab22 complexed SARS-CoV-2 spike | |||||||||
Map data | Structure of Fab22 complexed SARS-CoV-2 spike | |||||||||
Sample |
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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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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: 3.97 Å | |||||||||
Authors | Hsieh C-L / McLellan JS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep / Year: 2021 Title: Stabilized coronavirus spike stem elicits a broadly protective antibody. Authors: Ching-Lin Hsieh / Anne P Werner / Sarah R Leist / Laura J Stevens / Ester Falconer / Jory A Goldsmith / Chia-Wei Chou / Olubukola M Abiona / Ande West / Kathryn Westendorf / Krithika ...Authors: Ching-Lin Hsieh / Anne P Werner / Sarah R Leist / Laura J Stevens / Ester Falconer / Jory A Goldsmith / Chia-Wei Chou / Olubukola M Abiona / Ande West / Kathryn Westendorf / Krithika Muthuraman / Ethan J Fritch / Kenneth H Dinnon / Alexandra Schäfer / Mark R Denison / James D Chappell / Ralph S Baric / Barney S Graham / Kizzmekia S Corbett / Jason S McLellan / Abstract: Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, ...Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, we use structure-guided protein engineering to remove the S1 subunit from the Middle East respiratory syndrome (MERS)-CoV spike (S) glycoprotein and develop stabilized stem (SS) antigens. Vaccination with MERS SS elicits cross-reactive β-CoV antibody responses and protects mice against lethal MERS-CoV challenge. High-throughput screening of antibody-secreting cells from MERS SS-immunized mice led to the discovery of a panel of cross-reactive monoclonal antibodies. Among them, antibody IgG22 binds with high affinity to both MERS-CoV and severe acute respiratory syndrome (SARS)-CoV-2 S proteins, and a combination of electron microscopy and crystal structures localizes the epitope to a conserved coiled-coil region in the S2 subunit. Passive transfer of IgG22 protects mice against both MERS-CoV and SARS-CoV-2 challenge. Collectively, these results provide a proof of principle for cross-reactive CoV antibodies and inform the development of pan-CoV vaccines and therapeutic 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_25073.map.gz | 290.8 MB | EMDB map data format | |
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Header (meta data) | emd-25073-v30.xml emd-25073.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25073_fsc.xml | 15 KB | Display | FSC data file |
Images | emd_25073.png | 46.3 KB | ||
Others | emd_25073_half_map_1.map.gz emd_25073_half_map_2.map.gz | 285.7 MB 285.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25073 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25073 | HTTPS FTP |
-Validation report
Summary document | emd_25073_validation.pdf.gz | 466.2 KB | Display | EMDB validaton report |
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Full document | emd_25073_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | emd_25073_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | emd_25073_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25073 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25073 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25073.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of Fab22 complexed SARS-CoV-2 spike | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 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 1
File | emd_25073_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_25073_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : complex of Fab22 bound to SARS-CoV-2 spike
Entire | Name: complex of Fab22 bound to SARS-CoV-2 spike |
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Components |
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-Supramolecule #1: complex of Fab22 bound to SARS-CoV-2 spike
Supramolecule | Name: complex of Fab22 bound to SARS-CoV-2 spike / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 167.3 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.37 mg/mL |
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Buffer | pH: 8 / Details: 2 mM Tris pH 8.0, 200 mM NaCl, 0.02% NaN3 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: blotted for 3.5 seconds with -4 force in a Vitrobot Mark IV and plunge-frozen into liquid ethane. |
Details | purified SARS-CoV-2 S (HexaPro variant) complexed with 2-fold molar excess of Fab22 was diluted to a concentration of 0.37 mg/mL in 2 mM Tris pH 8.0, 200 mM NaCl, 0.02% NaN3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |