+Open data
-Basic information
Entry | Database: PDB / ID: 8bg6 | |||||||||||||||||||||
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Title | SARS-CoV-2 S protein in complex with pT1644 Fab | |||||||||||||||||||||
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 / 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 / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.11 Å | |||||||||||||||||||||
Authors | Stroeh, L. / Hansen, G. / Vollmer, B. / Krey, T. / Benecke, T. / Gruenewald, K. | |||||||||||||||||||||
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 | 8bg6.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bg6.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bg6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8bg6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8bg6_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 8bg6_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/8bg6 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/8bg6 | HTTPS FTP |
-Related structure data
Related structure data | 16024MC 8becC 8bg1C 8bg2C 8bg3C 8bg4C 8bg5C 8bg8C M: map data used to model this data 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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-Components
#1: Antibody | Mass: 24038.920 Da / Num. of mol.: 1 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) |
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#2: Antibody | Mass: 23570.016 Da / Num. of mol.: 1 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) |
#3: Protein | Mass: 140749.328 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 / Cell line (production host): HEK293ExPi / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Conc.: 0.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||
3D reconstruction | Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 440062 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||
Refinement | Cross valid method: NONE |