6WPS | pdb_00006wps

Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment

• PDB DOI: https://doi.org/10.2210/pdb6WPS/pdb
• EM Map EMD-21864: EMDB EMDataResource

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


• Deposited: 2020-04-27 Released: 2020-05-27 
• Deposition Author(s): Pinto, D., Park, Y.J., Beltramello, M., Walls, A.C., Tortorici, M.A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., Peter, A., Guarino, B., Spreafico, R., Cameroni, E., Case, J.B., Chen, R.E., Havenar-Daughton, C., Snell, G., Virgin, H.W., Lanzavecchia, A., Diamond, M.S., Fink, K., Veesler, D., Corti, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody.

Pinto, D., Park, Y.J., Beltramello, M., Walls, A.C., Tortorici, M.A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., Peter, A., Guarino, B., Spreafico, R., Cameroni, E., Case, J.B., Chen, R.E., Havenar-Daughton, C., Snell, G., Telenti, A., Virgin, H.W., Lanzavecchia, A., Diamond, M.S., Fink, K., Veesler, D., Corti, D.

(2020) Nature 583: 290-295

• PubMed: 32422645 
• DOI: https://doi.org/10.1038/s41586-020-2349-y
• Primary Citation Related Structures: 
  6WPS, 6WPT, 6WS6


• PubMed Abstract: 
  

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus that is responsible for the current pandemic of coronavirus disease 2019 (COVID-19), which has resulted in more than 3.7 million infections and 260,000 deaths as of 6 May 2020 ^1,2 . Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe several monoclonal antibodies that target the S glycoprotein of SARS-CoV-2, which we identified from memory B cells of an individual who was infected with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. One antibody (named S309) potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2, by engaging the receptor-binding domain of the S glycoprotein. Using cryo-electron microscopy and binding assays, we show that S309 recognizes an epitope containing a glycan that is conserved within the Sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails that include S309 in combination with other antibodies that we identified further enhanced SARS-CoV-2 neutralization, and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and antibody cocktails containing S309 for prophylaxis in individuals at a high risk of exposure or as a post-exposure therapy to limit or treat severe disease.

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Organizational Affiliation: 
• Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France.
Vir Biotechnology, San Francisco, CA, USA.
Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.
Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 516.51 kDa 
• Atom Count: 28,116 
• Modeled Residue Count: 3,540 
• Deposited Residue Count: 4,545 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
spike glycoprotein	A, D [auth B], G [auth E]	1,281	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 16		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 neutralizing antibody heavy chain	B [auth H], E [auth C], H [auth F]	127	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 neutralizing antibody light chain	C [auth L], F [auth D], I [auth G]	107	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	J [auth I], K [auth J], L [auth K], M, O, P, Q, R, T, U, V, W	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	N, S, X	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	AA [auth A], AB [auth E], BA [auth A], BB [auth E], CA [auth A], CB [auth E], DA [auth A], DB [auth E], EA [auth A], EB [auth E], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth E], VA [auth E], WA [auth E], XA [auth E], Y [auth A], YA [auth E], Z [auth A], ZA [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: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Rosetta

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Pinto, D., Park, Y.J., Beltramello, M., Walls, A.C., Tortorici, M.A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., Peter, A., Guarino, B., Spreafico, R., Cameroni, E., Case, J.B., Chen, R.E., Havenar-Daughton, C., Snell, G., Virgin, H.W., Lanzavecchia, A., Diamond, M.S., Fink, K., Veesler, D., Corti, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	120553

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-01-20
  Changes: Structure summary
• Version 2.2: 2021-05-19
  Changes: Database references
• Version 2.3: 2024-11-20
  Changes: Data collection, Database references, Refinement description, Structure summary