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- PDB-8bg5: Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV -
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Open data
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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 | |||||||||||||||||||||
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![]() | PROTEIN BINDING / PROTEIN BINDING/IMMUNE SYSTEM | |||||||||||||||||||||
Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 | ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Hansen, G. / Ssebyatika, G.L. / Krey, T. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 406.4 KB | Display | ![]() |
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PDB format | ![]() | 273.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481 KB | Display | ![]() |
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Full document | ![]() | 484.2 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8becC ![]() 8bg1C ![]() 8bg2C ![]() 8bg3C ![]() 8bg4C ![]() 8bg6C ![]() 8bg8C ![]() 7choS ![]() 7kgjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() #2: Protein | Mass: 25349.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Cell line (production host): S2 / Production host: ![]() ![]() #3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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