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- PDB-7y3o: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y3o | ||||||
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Title | Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / 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 / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rao, X. / Gao, F. / 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 | ![]() | 183.8 KB | Display | ![]() |
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PDB format | ![]() | 115.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457 KB | Display | ![]() |
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Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y3nC ![]() 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: Antibody | Mass: 24154.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23343.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 21772.391 Da / Num. of mol.: 1 / Fragment: RBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Imidazole malate, pH 7.0, 20% w/v PEG 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: Jan 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 45625 / % possible obs: 99.96 % / Redundancy: 12.6 % / Biso Wilson estimate: 36.25 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 1.189 / Num. unique obs: 5159 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LZG, 4TSA Resolution: 2.1→46.13 Å / SU ML: 0.2684 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.427 / Stereochemistry target values: GeoStd + Monomer Library
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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: 40.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.13 Å
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Refine LS restraints |
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LS refinement shell |
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