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- PDB-7xs8: Crystal structure of SARS-CoV-2 spike receptor binding domain bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xs8 | ||||||
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Title | Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-1H1 Fab | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / 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 / 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 / membrane fusion / Attachment and Entry / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, X. / Wang, Z. | ||||||
Funding support | 1items
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![]() | ![]() Title: Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants. Authors: Ju, B. / Zhang, Q. / Wang, Z. / Aw, Z.Q. / Chen, P. / Zhou, B. / Wang, R. / Ge, X. / Lv, Q. / Cheng, L. / Zhang, R. / Wong, Y.H. / Chen, H. / Wang, H. / Shan, S. / Liao, X. / Shi, X. / Liu, ...Authors: Ju, B. / Zhang, Q. / Wang, Z. / Aw, Z.Q. / Chen, P. / Zhou, B. / Wang, R. / Ge, X. / Lv, Q. / Cheng, L. / Zhang, R. / Wong, Y.H. / Chen, H. / Wang, H. / Shan, S. / Liao, X. / Shi, X. / Liu, L. / Chu, J.J.H. / Wang, X. / Zhang, Z. / Zhang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.1 KB | Display | ![]() |
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PDB format | ![]() | 97.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 889 KB | Display | ![]() |
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Full document | ![]() | 894.3 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xsaC ![]() 7xsbC ![]() 7xscC ![]() 6m0jS 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: 22811.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 21772.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
#3: Antibody | Mass: 23039.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.1 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.4, 13% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 23, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 22719 / % possible obs: 98.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.097 / Rrim(I) all: 0.251 / Χ2: 1.257 / Net I/σ(I): 3.8 / Num. measured all: 147555 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M0J Resolution: 2.8→48 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.15 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.64 Å2 / Biso mean: 54.6924 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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