+Open data
-Basic information
Entry | Database: PDB / ID: 7bwj | ||||||
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Title | crystal structure of SARS-CoV-2 antibody with RBD | ||||||
Components |
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Keywords | VIRAL PROTEIN / spike / receptor binding domain / antibody | ||||||
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 / 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 / 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 / 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 | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Wang, X. / Ge, J. | ||||||
Citation | Journal: Nature / Year: 2020 Title: Human neutralizing antibodies elicited by SARS-CoV-2 infection. Authors: Ju, B. / Zhang, Q. / Ge, J. / Wang, R. / Sun, J. / Ge, X. / Yu, J. / Shan, S. / Zhou, B. / Song, S. / Tang, X. / Yu, J. / Lan, J. / Yuan, J. / Wang, H. / Zhao, J. / Zhang, S. / Wang, Y. / ...Authors: Ju, B. / Zhang, Q. / Ge, J. / Wang, R. / Sun, J. / Ge, X. / Yu, J. / Shan, S. / Zhou, B. / Song, S. / Tang, X. / Yu, J. / Lan, J. / Yuan, J. / Wang, H. / Zhao, J. / Zhang, S. / Wang, Y. / Shi, X. / Liu, L. / Zhao, J. / Wang, X. / Zhang, Z. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bwj.cif.gz | 259.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bwj.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bwj_validation.pdf.gz | 468.2 KB | Display | wwPDB validaton report |
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Full document | 7bwj_full_validation.pdf.gz | 475.8 KB | Display | |
Data in XML | 7bwj_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 7bwj_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/7bwj ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bwj | HTTPS FTP |
-Related structure data
Related structure data | 6m0jS S: Starting model for refinement |
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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
#1: Protein | Mass: 24600.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2 |
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#2: Antibody | Mass: 22686.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 24122.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M magnesium formate dihydrate, 0.1M sodium acetate trihydrate, pH 4.0, 18% PEG 5000 mme |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→90.15 Å / Num. obs: 17230 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.85→2.92 Å / Rmerge(I) obs: 1.452 / Num. unique obs: 1273 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M0J Resolution: 2.85→59.552 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.67 / 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: 160.89 Å2 / Biso mean: 74.4316 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→59.552 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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