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Yorodumi- PDB-7djz: Crystal structure of SARS-CoV-2 Spike RBD in complex with MW01 Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 7djz | ||||||
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Title | Crystal structure of SARS-CoV-2 Spike RBD in complex with MW01 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / Spike / RBD / Antibody / ADE / VIRUS / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å | ||||||
Authors | Wang, J. / Jiao, S. / Wang, R. / Zhang, J. / Zhang, M. / Wang, M. | ||||||
Citation | Journal: Commun Biol / Year: 2022 Title: Antibody-dependent enhancement (ADE) of SARS-CoV-2 pseudoviral infection requires Fc gamma RIIB and virus-antibody complex with bivalent interaction. Authors: Wang, S. / Wang, J. / Yu, X. / Jiang, W. / Chen, S. / Wang, R. / Wang, M. / Jiao, S. / Yang, Y. / Wang, W. / Chen, H. / Chen, B. / Gu, C. / Liu, C. / Wang, A. / Wang, M. / Li, G. / Guo, C. / ...Authors: Wang, S. / Wang, J. / Yu, X. / Jiang, W. / Chen, S. / Wang, R. / Wang, M. / Jiao, S. / Yang, Y. / Wang, W. / Chen, H. / Chen, B. / Gu, C. / Liu, C. / Wang, A. / Wang, M. / Li, G. / Guo, C. / Liu, D. / Zhang, J. / Zhang, M. / Wang, L. / Gui, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7djz.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7djz.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 7djz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/7djz ftp://data.pdbj.org/pub/pdb/validation_reports/dj/7djz | HTTPS FTP |
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-Related structure data
Related structure data | 7dk0C 6jjpS 6lzgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23804.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 23146.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
-Protein / Sugars , 2 types, 2 molecules C
#3: Protein | Mass: 25122.336 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2 |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 318 molecules
#4: Chemical | ChemComp-CIT / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.56 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate, pH 5.6, 18% (w/v) polyethylene glycol (PEG) 4000, 14% (v/v) 2-propanol, and 0.01 M barium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.397→50 Å / Num. obs: 33331 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.048 / Rrim(I) all: 0.156 / Χ2: 1.017 / Net I/σ(I): 4.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LZG, 6JJP Resolution: 2.397→39.679 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1 / 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: 105.33 Å2 / Biso mean: 47.1609 Å2 / Biso min: 18.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.397→39.679 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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