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Yorodumi- PDB-7tty: Crystal structure of potent neutralizing antibody 10-40 in comple... -
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-Basic information
Entry | Database: PDB / ID: 7tty | ||||||
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Title | Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SarbecoVirus / WIV1 RBD / Viral protein / Spike glycoprotein / Receptor Binding Protein / Neutralizing antibody / potent / 10-40 / Fab / 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 | Bat SARS-like coronavirus WIV1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å | ||||||
Authors | Reddem, E.R. / Shapiro, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses. Authors: Lihong Liu / Sho Iketani / Yicheng Guo / Eswar R Reddem / Ryan G Casner / Manoj S Nair / Jian Yu / Jasper F-W Chan / Maple Wang / Gabriele Cerutti / Zhiteng Li / Nicholas C Morano / Candace ...Authors: Lihong Liu / Sho Iketani / Yicheng Guo / Eswar R Reddem / Ryan G Casner / Manoj S Nair / Jian Yu / Jasper F-W Chan / Maple Wang / Gabriele Cerutti / Zhiteng Li / Nicholas C Morano / Candace D Castagna / Laura Corredor / Hin Chu / Shuofeng Yuan / Vincent Kwok-Man Poon / Chris Chun-Sing Chan / Zhiwei Chen / Yang Luo / Marcus Cunningham / Alejandro Chavez / Michael T Yin / David S Perlin / Moriya Tsuji / Kwok-Yung Yuen / Peter D Kwong / Zizhang Sheng / Yaoxing Huang / Lawrence Shapiro / David D Ho / Abstract: The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related ...The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tty.cif.gz | 435.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tty.ent.gz | 302 KB | Display | PDB format |
PDBx/mmJSON format | 7tty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tty_validation.pdf.gz | 722.2 KB | Display | wwPDB validaton report |
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Full document | 7tty_full_validation.pdf.gz | 728.3 KB | Display | |
Data in XML | 7tty_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 7tty_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7tty ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7tty | HTTPS FTP |
-Related structure data
Related structure data | 7sd5SC 7si2C 7ttmC 7ttxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21979.701 Da / Num. of mol.: 1 / Fragment: receptor-binding domain (UNP residues 322-515) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bat SARS-like coronavirus WIV1 / Production host: Homo sapiens (human) / References: UniProt: U5WI05 |
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#2: Antibody | Mass: 24794.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 22938.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate, pH 5.5, 20% propanol, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.11→91.69 Å / Num. obs: 11493 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 79.5 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.165 / Rrim(I) all: 0.4 / Net I/σ(I): 2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7SD5 Resolution: 3.11→91.69 Å / SU ML: 0.5979 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8545 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: 70 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.11→91.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.269 Å / Origin y: -3.966 Å / Origin z: 24.866 Å
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Refinement TLS group |
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