8ERQ | pdb_00008erq

SARS-CoV-2 BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment (local refinement of the RBD and S2X324)

• PDB DOI: https://doi.org/10.2210/pdb8ERQ/pdb
• EM Map EMD-28558: EMDB EMDataResource

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


• Deposited: 2022-10-12 Released: 2022-10-26 
• Deposition Author(s): Park, Y.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
• 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: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.

Park, Y.J., Pinto, D., Walls, A.C., Liu, Z., De Marco, A., Benigni, F., Zatta, F., Silacci-Fregni, C., Bassi, J., Sprouse, K.R., Addetia, A., Bowen, J.E., Stewart, C., Giurdanella, M., Saliba, C., Guarino, B., Schmid, M.A., Franko, N.M., Logue, J.K., Dang, H.V., Hauser, K., di Iulio, J., Rivera, W., Schnell, G., Rajesh, A., Zhou, J., Farhat, N., Kaiser, H., Montiel-Ruiz, M., Noack, J., Lempp, F.A., Janer, J., Abdelnabi, R., Maes, P., Ferrari, P., Ceschi, A., Giannini, O., de Melo, G.D., Kergoat, L., Bourhy, H., Neyts, J., Soriaga, L., Purcell, L.A., Snell, G., Whelan, S.P.J., Lanzavecchia, A., Virgin, H.W., Piccoli, L., Chu, H.Y., Pizzuto, M.S., Corti, D., Veesler, D.

(2022) Science 378: 619-627

• PubMed: 36264829 
• DOI: https://doi.org/10.1126/science.adc9127
• Primary Citation Related Structures: 
  8ERQ, 8ERR


• PubMed Abstract: 
  

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
Vir Biotechnology, San Francisco, CA, USA.
KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium.
Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland.
Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland.
Clinical School, University of New South Wales, Sydney, New South Wales, Australia.
Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland.
Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland.
Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland.
Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.
Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France.
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.

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: 166.81 kDa 
• Atom Count: 3,178 
• Modeled Residue Count: 423 
• Deposited Residue Count: 1,503 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S2X324 Fab heavy chain	A [auth H]	119	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S2X324 Fab light chain	B [auth L]	110	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A]	1,274	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 36  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 A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Park, Y.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120553

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2022-11-23
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Structure summary