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- PDB-7y3n: Crystal structure of SARS-CoV receptor binding domain in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y3n | ||||||
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Title | Crystal structure of SARS-CoV receptor binding domain in complex with human antibody BIOLS56 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rao, X. / Chai, Y. / Wu, Y. / Gao, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2. Authors: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / ...Authors: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / Zou, W. / Li, W. / Wang, Q. / Gao, G.F. / Wu, Y. / Dai, L. / Gao, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 400.5 KB | Display | ![]() |
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PDB format | ![]() | 298.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7y3oC ![]() 8hrdC ![]() 4tsaS ![]() 6lzgS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25863.234 Da / Num. of mol.: 3 / Fragment: receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: S, 2 / Cell line (production host): HEK293 / Production host: ![]() #2: Antibody | Mass: 25340.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 23430.943 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 20% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.9, 20% w/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→50 Å / Num. obs: 64593 / % possible obs: 99.3 % / Redundancy: 12.5 % / Biso Wilson estimate: 55.17 Å2 / Rmerge(I) obs: 0.281 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.97→3.11 Å / Rmerge(I) obs: 0.898 / Num. unique obs: 64593 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LZG, 4TSA Resolution: 2.97→47.39 Å / SU ML: 0.3884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8357 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: 52.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.97→47.39 Å
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Refine LS restraints |
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LS refinement shell |
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