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Yorodumi- PDB-7l5b: Crystallographic structure of neutralizing antibody 2-15 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l5b | ||||||
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Title | Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD). | ||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / Spike protein S1 / receptor binding protein SARS COV-2 / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | ||||||
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å | ||||||
Authors | Reddem, E.R. / Shapiro, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Rep / Year: 2021 Title: Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class. Authors: Micah Rapp / Yicheng Guo / Eswar R Reddem / Jian Yu / Lihong Liu / Pengfei Wang / Gabriele Cerutti / Phinikoula Katsamba / Jude S Bimela / Fabiana A Bahna / Seetha M Mannepalli / Baoshan ...Authors: Micah Rapp / Yicheng Guo / Eswar R Reddem / Jian Yu / Lihong Liu / Pengfei Wang / Gabriele Cerutti / Phinikoula Katsamba / Jude S Bimela / Fabiana A Bahna / Seetha M Mannepalli / Baoshan Zhang / Peter D Kwong / Yaoxing Huang / David D Ho / Lawrence Shapiro / Zizhang Sheng / Abstract: Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies yet identified. To ...Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determine the structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three use VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy-chain N53I-enhancing binding and light-chain tyrosines recognizing F486. Despite these similarities, class members bind both RBD-up and -down conformations of the spike, with a subset of antibodies using elongated CDRH3s to recognize glycan N343 on a neighboring RBD-a quaternary interaction accommodated by an increase in RBD separation of up to 12 Å. The VH1-2 antibody class, thus, uses modular recognition encoded by modular genetic elements to effect potent neutralization, with the VH-gene component specifying recognition of RBD and the CDRH3 component specifying quaternary interactions. #1: Journal: Biorxiv / Year: 2021 Title: Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class Authors: Rapp, M. / Guo, Y. / Reddem, E.R. / Liu, L. / Wang, P. / Yu, J. / Cerutti, G. / Bimela, J. / Bahna, F. / Mannepalli, S. / Zhang, B. / Kwong, P.D. / Ho, D.D. / Shapiro, L. / Sheng, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l5b.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l5b.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 7l5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/7l5b ftp://data.pdbj.org/pub/pdb/validation_reports/l5/7l5b | HTTPS FTP |
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-Related structure data
Related structure data | 7l56C 7l57C 7l58C 7bz5S 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 | Mass: 26898.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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#2: Protein | Mass: 24333.307 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: 22755.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes, 70 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→102.49 Å / Num. obs: 27227 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.951 / Rmerge(I) obs: 0.111 / Net I/σ(I): 1.7 |
Reflection shell | Resolution: 3.18→3.88 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 4388 / CC1/2: 0.992 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7bz5 Resolution: 3.18→102.49 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.18→102.49 Å
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Refine LS restraints |
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LS refinement shell |
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