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- PDB-7c01: Molecular basis for a potent human neutralizing antibody targetin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c01 | |||||||||||||||
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Title | Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD | |||||||||||||||
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![]() | VIRAL PROTEIN / SARS-CoV-2 / RBD / neutralizing antibodies / molecular basis | |||||||||||||||
Function / homology | ![]() 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 / Attachment and Entry / membrane fusion / 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 | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Shi, R. / Qi, J. / Wang, Q. / Gao, F.G. / Yan, J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Authors: Shi, R. / Shan, C. / Duan, X. / Chen, Z. / Liu, P. / Song, J. / Song, T. / Bi, X. / Han, C. / Wu, L. / Gao, G. / Hu, X. / Zhang, Y. / Tong, Z. / Huang, W. / Liu, W.J. / Wu, G. / Zhang, B. / ...Authors: Shi, R. / Shan, C. / Duan, X. / Chen, Z. / Liu, P. / Song, J. / Song, T. / Bi, X. / Han, C. / Wu, L. / Gao, G. / Hu, X. / Zhang, Y. / Tong, Z. / Huang, W. / Liu, W.J. / Wu, G. / Zhang, B. / Wang, L. / Qi, J. / Feng, H. / Wang, F.S. / Wang, Q. / Gao, G.F. / Yuan, Z. / Yan, J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 547.9 KB | Display | ![]() |
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PDB format | ![]() | 400.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25951.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Cell line (production host): HEK293 / Production host: ![]() #2: Antibody | Mass: 24950.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 23718.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24 % w/v PEG 1500, 20 % v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 36863 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 63.8 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.88→2.95 Å / Num. unique obs: 2670 / CC1/2: 0.64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LGZ, 4TSA Resolution: 2.88→34.83 Å / SU ML: 0.3529 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2768
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→34.83 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 |
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