8BG6 | pdb_00008bg6

SARS-CoV-2 S protein in complex with pT1644 Fab

• PDB DOI: https://doi.org/10.2210/pdb8BG6/pdb
• EM Map EMD-16024: EMDB EMDataResource

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


• Deposited: 2022-10-27 Released: 2023-11-08 
• Deposition Author(s): Stroeh, L., Hansen, G., Vollmer, B., Krey, T., Benecke, T., Gruenewald, K.
• 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: 4.11 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: 188.58 kDa 
• Atom Count: 3,124 
• Modeled Residue Count: 398 
• Deposited Residue Count: 1,712 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1644 Fab heavy chain	A	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1644 Fab light chain	B	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth E]	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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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
• Version 1.2: 2025-07-02
  Changes: Data collection