9H6U | pdb_00009h6u

SARS-CoV-2 S protein in complex with pT1679 Fab

• PDB DOI: https://doi.org/10.2210/pdb9H6U/pdb
• EM Map EMD-51901: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, Homo sapiens
• Expression System: Homo sapiens, Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2024-10-25 Released: 2025-07-23 
• 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: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A critical residue in a conserved RBD epitope determines neutralization breadth of pan-sarbecovirus antibodies

Stein, C.S., Hansen, G., Ssebyatika, G.L., Benecke, T., Stroeh, L., Rajak, M.K., Menz, S., Waldmann, J.-Y., Vollmer, B., Tipp, S., Ochulor, O., Herold, E., Schwarzloh, B., Mutschall, D., Zischke, J.-Y., Cordes, A., Schneider, T., Hinrichs, I., Blasczyk, R., Kleine-Weber, H., Hoffmann, M., Klein, F., Hoeper, M., Kaiser, F.K., Gonzalez-Hernandez, M., Armando, F.K., Ciurkiewicz, M., Beythien, G., Poehlmann, S., Baumgaertner, W., Gruenewald, K., Osterhaus, A., Krey, T., Schulz, 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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 191.52 kDa 
• Atom Count: 3,349 
• Modeled Residue Count: 434 
• Deposited Residue Count: 1,751 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin	A	1,273	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 6  Gene Names: S, 2, wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104
UniProt Groups	P0DTC2P10104
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1679 Fab heavy chain	B [auth H]	259	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1679 Fab light chain	C [auth L]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Hansen, G., Benecke, T., Vollmer, B., Gruenewald, K., Krey, T.

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Funding Organization	Location	Grant Number
Other government		14-76103-184 CORONA-12/20
Other government		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)
Other government		14-76403-184
Other government		14-76103-184
Other government		MWK TiHO SARS-COV-2

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release