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Yorodumi- PDB-7bz5: Structure of COVID-19 virus spike receptor-binding domain complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bz5 | ||||||
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Title | Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / covid-19 antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Wu, Y. / Qi, J. / Gao, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Science / Year: 2020 Title: A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. Authors: Wu, Y. / Wang, F. / Shen, C. / Peng, W. / Li, D. / Zhao, C. / Li, Z. / Li, S. / Bi, Y. / Yang, Y. / Gong, Y. / Xiao, H. / Fan, Z. / Tan, S. / Wu, G. / Tan, W. / Lu, X. / Fan, C. / Wang, Q. / ...Authors: Wu, Y. / Wang, F. / Shen, C. / Peng, W. / Li, D. / Zhao, C. / Li, Z. / Li, S. / Bi, Y. / Yang, Y. / Gong, Y. / Xiao, H. / Fan, Z. / Tan, S. / Wu, G. / Tan, W. / Lu, X. / Fan, C. / Wang, Q. / Liu, Y. / Zhang, C. / Qi, J. / Gao, G.F. / Gao, F. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bz5.cif.gz | 269.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bz5.ent.gz | 212.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/7bz5 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/7bz5 | HTTPS FTP |
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-Related 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: 25951.219 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: 23442.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 23745.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
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: 3.23 Å3/Da / Density % sol: 61.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.15 M ammonium sulfate, 0.1 M MES pH 6, 15% w/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97981 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 80095 / % possible obs: 99.41 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.044 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.84→1.92 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7992 / CC1/2: 0.662 / Rpim(I) all: 0.526 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LZG, 4TSA Resolution: 1.84→28.49 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.9 Å2 / Biso mean: 39.9588 Å2 / Biso min: 17.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→28.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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