8BG8 | pdb_00008bg8

SARS-CoV-2 S protein in complex with pT1696 Fab

• PDB DOI: https://doi.org/10.2210/pdb8BG8/pdb
• EM Map EMD-16026: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens, Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2022-10-27 Released: 2023-11-08 
• Deposition Author(s): Hansen, G., Benecke, T., Vollmer, B., Gruenewald, K., Krey, T.
• Funding Organization(s): Other government, German Federal Ministry for Education and Research, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?

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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 192.98 kDa 
• Atom Count: 3,319 
• Modeled Residue Count: 421 
• Deposited Residue Count: 1,754 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1696 Fab heavy chain	B [auth H]	264	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1696 Fab light chain	C [auth L]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Hansen, G., Benecke, T., Vollmer, B., Gruenewald, K., Krey, T.

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Funding Organization	Location	Grant Number
Other government	Germany	14-76103-184 CORONA-12/20
Other government	Germany	14-76103-184 CORONA-15/20
German Federal Ministry for Education and Research	Germany	COVIM (FKZ: 01KX2021)
German Federal Ministry for Education and Research	Germany	RAPID (FKZ: 01KI1723G)
German Research Foundation (DFG)	Germany	EXC 2155
German Research Foundation (DFG)	Germany	2485 VIPER (398066876/GRK 2485/1)

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary