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Yorodumi- PDB-7deu: Crystal structure of SARS-CoV-2 RBD in complex with a neutralizin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7deu | |||||||||
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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 / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / symbiont-mediated suppression of host innate immune response / 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 | Severe acute respiratory syndrome coronavirus 2 Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Zhang, Z. / 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 | 7deu.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7deu.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 7deu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7deu ftp://data.pdbj.org/pub/pdb/validation_reports/de/7deu | HTTPS FTP |
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-Related structure data
Related structure data | 7deoC 7detC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23159.947 Da / Num. of mol.: 1 / 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 |
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#2: Antibody | Mass: 27374.025 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#3: Sugar | ChemComp-NAG / |
#4: 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: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.8M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5, 0.5% w/v Polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SwissFEL ARAMIS / Beamline: ESA / 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: 2.1→50 Å / Num. obs: 34362 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 2765 / CC1/2: 0.975 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CJF Resolution: 2.1→47.703 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.72 / 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: 106.49 Å2 / Biso mean: 45.6859 Å2 / Biso min: 20.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→47.703 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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