+Open data
-Basic information
Entry | Database: PDB / ID: 7s3m | ||||||
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Title | MERS-CoV S stem helix peptide bound to Fab22 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Spike / Fusion / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Goldsmith, J.A. / McLellan, J.S. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s3m.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s3m.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 7s3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s3m_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 7s3m_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 7s3m_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 7s3m_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/7s3m ftp://data.pdbj.org/pub/pdb/validation_reports/s3/7s3m | HTTPS FTP |
-Related structure data
Related structure data | 7s3nC 7m55S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1834.909 Da / Num. of mol.: 1 / Fragment: stem helix peptide (UNP residues 1230-1244) / Source method: obtained synthetically Source: (synth.) Middle East respiratory syndrome-related coronavirus References: UniProt: R9UQ53 |
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#2: Antibody | Mass: 23892.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 24055.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG1000, 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→71.84 Å / Num. obs: 33665 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 53.88 Å2 / CC1/2: 0.988 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3507 / CC1/2: 0.927 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7M55 Resolution: 2.4→53.33 Å / SU ML: 0.426 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.8502 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→53.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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