8QQ0

SARS-CoV-2 S protein bound to neutralising antibody UZGENT_A3

• PDB DOI: https://doi.org/10.2210/pdb8QQ0/pdb
• EM Map EMD-18571: EMDB EMDataResource

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


• Deposited: 2023-10-03 Released: 2024-01-31 
• Deposition Author(s): Remaut, H., Reiter, D., Vandenkerckhove, L., Acar, D.D., Witkowski, W., Gerlo, S.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.

Acar, D.D., Witkowski, W., Wejda, M., Wei, R., Desmet, T., Schepens, B., De Cae, S., Sedeyn, K., Eeckhaut, H., Fijalkowska, D., Roose, K., Vanmarcke, S., Poupon, A., Jochmans, D., Zhang, X., Abdelnabi, R., Foo, C.S., Weynand, B., Reiter, D., Callewaert, N., Remaut, H., Neyts, J., Saelens, X., Gerlo, S., Vandekerckhove, L.

(2024) EBioMedicine 100: 104960-104960

• PubMed: 38232633 
• DOI: https://doi.org/10.1016/j.ebiom.2023.104960
• Primary Citation of Related Structures:  
  8QPR, 8QQ0


• PubMed Abstract: 
  

  SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes.

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Organizational Affiliation: 

HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.

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 and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 192.76 kDa 
• Atom Count: 5,677 
• Modelled Residue Count: 715 
• Deposited Residue Count: 1,733 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin	A	1,288	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 10  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG light chain - FAB	B [auth D]	216	Homo sapiens	Mutation(s): 0  Gene Names: IgG

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG heavy chain - FAB	C [auth E]	229	Homo sapiens	Mutation(s): 0  Gene Names: IgG

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth a], E [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth c], G [auth F], H [auth e]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [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: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.18.2_3874:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Remaut, H., Reiter, D., Vandenkerckhove, L., Acar, D.D., Witkowski, W., Gerlo, S.

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Funding Organization	Location	Grant Number
Other government	Belgium	--

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release