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Yorodumi- PDB-8bg5: Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bg5 | |||||||||||||||||||||
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Title | Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV | |||||||||||||||||||||
Components |
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Keywords | PROTEIN BINDING / PROTEIN BINDING/IMMUNE SYSTEM | |||||||||||||||||||||
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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||||||||||||||
Authors | Hansen, G. / Ssebyatika, G.L. / Krey, T. | |||||||||||||||||||||
Funding support | Germany, 6items
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Citation | Journal: To be published Title: Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses? Authors: Stein, C.S. / Hansen, G. / Ssebyatika, G.L. / Stroeh, L. / Benecke, T. / Menz, S. / Waldmann, J.-Y. / Vollmer, B. / Tipp, S. / Ochulor, O. / Herold, E. / Schwarzloh, B. / Mutschall, D. / ...Authors: Stein, C.S. / Hansen, G. / Ssebyatika, G.L. / Stroeh, L. / Benecke, T. / Menz, S. / Waldmann, J.-Y. / Vollmer, B. / Tipp, S. / Ochulor, O. / Herold, E. / Schwarzloh, B. / Mutschall, D. / Zischke, J.-Y. / Cordes, A. / Puppe, W. / Schneider, T. / Hinrichs, I. / Blasczyk, R. / Kleine-Weber, H. / Hoffmann, M. / Hoeper, M. / Kaiser, F.K. / Gonzalez-Hernandez, M. / Armando, F.K. / Ciurkiewicz, M. / Beythien, G. / Poehlmann, S. / Baumgaertner, W. / Gruenewald, K. / Osterhaus, A. / Schulz, T. / Krey, T. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bg5.cif.gz | 406.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bg5.ent.gz | 273.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/8bg5 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/8bg5 | HTTPS FTP |
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-Related structure data
Related structure data | 8becC 8bg1C 8bg2C 8bg3C 8bg4C 8bg6C 8bg8C 7choS 7kgjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: Antibody | Mass: 29485.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) #2: Protein | Mass: 25349.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0DTC2 #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: 3.4 Å3/Da / Density % sol: 63.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: pT1631-RBD at 15.8 mg/ml using 16 % PEG 4000, 100 mM Tris pH 8.5, 200 mM Li2SO4 as reservoir and micro seeds in 18% PEG 3350, 100 mM citrate pH 4, 200 mM Na3Cit stabilization solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→49.25 Å / Num. obs: 79963 / % possible obs: 99.75 % / Redundancy: 13.7 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.03156 / Rrim(I) all: 0.1174 / Net I/σ(I): 16.31 |
Reflection shell | Resolution: 2.05→2.123 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.667 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 7760 / CC1/2: 0.674 / CC star: 0.897 / Rpim(I) all: 0.4625 / Rrim(I) all: 1.731 / % possible all: 97.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KGJ, 7CHO Resolution: 2.05→49.25 Å / SU ML: 0.251 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7729 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→49.25 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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