7U0A | pdb_00007u0a

Crystal Structure of C77G12 Fab in complex with SARS-CoV-2 S fusion peptide

• PDB DOI: https://doi.org/10.2210/pdb7U0A/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-02-17 Released: 2022-08-03 
• Deposition Author(s): Tortorici, M.A., Veesler, D.
• Funding Organization(s): Partnership for Structural Biology (PSB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.

Low, J.S., Jerak, J., Tortorici, M.A., McCallum, M., Pinto, D., Cassotta, A., Foglierini, M., Mele, F., Abdelnabi, R., Weynand, B., Noack, J., Montiel-Ruiz, M., Bianchi, S., Benigni, F., Sprugasci, N., Joshi, A., Bowen, J.E., Stewart, C., Rexhepaj, M., Walls, A.C., Jarrossay, D., Morone, D., Paparoditis, P., Garzoni, C., Ferrari, P., Ceschi, A., Neyts, J., Purcell, L.A., Snell, G., Corti, D., Lanzavecchia, A., Veesler, D., Sallusto, F.

(2022) Science 377: 735-742

• PubMed: 35857703 
• DOI: https://doi.org/10.1126/science.abq2679
• Primary Citation Related Structures: 
  7SKZ, 7SL5, 7U09, 7U0A, 7U0E


• PubMed Abstract: 
  

  The coronavirus spike glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus spike proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors. These mAbs recognize the fusion peptide and acquire affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha- and betacoronaviruses, including animal coronaviruses WIV-1 and PDF-2180. Two selected mAbs also neutralize Omicron BA.1 and BA.2 authentic viruses and reduce viral burden and pathology in vivo. Structural and functional analyses showed that the fusion peptide-specific mAbs bound with different modalities to a cryptic epitope hidden in prefusion stabilized spike, which became exposed upon binding of angiotensin-converting enzyme 2 (ACE2) or ACE2-mimicking mAbs.

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Organizational Affiliation: 
• Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland.
Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland.
KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium.
KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, B-3000 Leuven, Belgium.
Vir Biotechnology, San Francisco, CA 94158, USA.
Howard Hughes Medical Institute, Seattle, WA 98195, USA.
Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland.
Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland.
Department of Internal Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland.
Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia.
Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland.
Clinical Trial Unit, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland.
Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland.
Global Virus Network, Baltimore, MD 21201, USA.
National Institute of Molecular Genetics, 20122 Milano, Italy.

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)

Macromolecule Content 

• Total Structure Weight: 48.98 kDa 
• Atom Count: 4,071 
• Modeled Residue Count: 451 
• Deposited Residue Count: 453 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 S fusion peptide	A	14	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain Fab C77G12	B [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain Fab C77G12	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.227	α = 90
b = 64.056	β = 93.33
c = 78.813	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Tortorici, M.A., Veesler, D.

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Funding Organization	Location	Grant Number
Partnership for Structural Biology (PSB)	France	SSGCID

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 2.0: 2022-08-10
  Changes: Advisory, Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2022-08-24
  Changes: Database references
• Version 2.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-13
  Changes: Structure summary