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Yorodumi- PDB-7det: Crystal structure of SARS-CoV-2 RBD in complex with a neutralizin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7det | |||||||||
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Title | Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv | |||||||||
Components |
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Keywords | VIRAL PROTEIN/ANTIVIRAL PROTEIN / SARS-CoV-2 / RBD / antibody / VIRAL PROTEIN / ANTIVIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL 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 / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Wang, Y. / Zhang, G. / Li, X. / Rao, Z. / Guo, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Plos Biol. / Year: 2021 Title: Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes. Authors: Fu, D. / Zhang, G. / Wang, Y. / Zhang, Z. / Hu, H. / Shen, S. / Wu, J. / Li, B. / Li, X. / Fang, Y. / Liu, J. / Wang, Q. / Zhou, Y. / Wang, W. / Li, Y. / Lu, Z. / Wang, X. / Nie, C. / Tian, ...Authors: Fu, D. / Zhang, G. / Wang, Y. / Zhang, Z. / Hu, H. / Shen, S. / Wu, J. / Li, B. / Li, X. / Fang, Y. / Liu, J. / Wang, Q. / Zhou, Y. / Wang, W. / Li, Y. / Lu, Z. / Wang, X. / Nie, C. / Tian, Y. / Chen, D. / Wang, Y. / Zhou, X. / Wang, Q. / Yu, F. / Zhang, C. / Deng, C. / Zhou, L. / Guan, G. / Shao, N. / Lou, Z. / Deng, F. / Zhang, H. / Chen, X. / Wang, M. / Liu, L. / Rao, Z. / Guo, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7det.cif.gz | 187.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7det.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 7det.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7det_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 7det_full_validation.pdf.gz | 486.2 KB | Display | |
Data in XML | 7det_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 7det_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7det ftp://data.pdbj.org/pub/pdb/validation_reports/de/7det | HTTPS FTP |
-Related structure data
Related structure data | 7deoC 7deuC 7cjfS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23159.947 Da / Num. of mol.: 2 / Fragment: RBD 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 #2: Antibody | Mass: 30431.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.91 Å3/Da / Density % sol: 35.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2M sodium chloride, 0.1M Tris pH 8.5, 29% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 41108 / % possible obs: 99.1 % / Redundancy: 10.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1853 / CC1/2: 0.815 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CJF Resolution: 2.2→46.472 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.22 / 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: 85.11 Å2 / Biso mean: 34.9729 Å2 / Biso min: 12.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→46.472 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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