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- PDB-8i5i: Crystal structure of SARS-CoV-2 delta variant spike receptor-bind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i5i | ||||||
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Title | Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / spike / coronavirus / viral protein / Fab / VIRUS / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamamoto, A. / Higashiura, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants. Authors: Shitaoka, K. / Higashiura, A. / Kawano, Y. / Yamamoto, A. / Mizoguchi, Y. / Hashiguchi, T. / Nishimichi, N. / Huang, S. / Ito, A. / Ohki, S. / Kanda, M. / Taniguchi, T. / Yoshizato, R. / ...Authors: Shitaoka, K. / Higashiura, A. / Kawano, Y. / Yamamoto, A. / Mizoguchi, Y. / Hashiguchi, T. / Nishimichi, N. / Huang, S. / Ito, A. / Ohki, S. / Kanda, M. / Taniguchi, T. / Yoshizato, R. / Azuma, H. / Kitajima, Y. / Yokosaki, Y. / Okada, S. / Sakaguchi, T. / Yasuda, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.8 KB | Display | ![]() |
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PDB format | ![]() | 203.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 469.8 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wn2C ![]() 7wnbC ![]() 7yowC ![]() 8i5hC 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: 25332.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Variant: delta / Production host: ![]() |
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#2: Antibody | Mass: 24241.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23119.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500 |
-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: Oct 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→67.21 Å / Num. obs: 7419 / % possible obs: 88.6 % / Redundancy: 17.8 % / Biso Wilson estimate: 77.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.05→3.47 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 371 / CC1/2: 0.73 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→67.21 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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