7K3Q | pdb_00007k3q

An ultra-potent human neutralizing antibody locks the SARS-CoV-2 spike in the closed conformation

• PDB DOI: https://doi.org/10.2210/pdb7K3Q/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2020-09-12 Released: 2020-10-07 
• Deposition Author(s): Snell, G., Czudnochowski, N., Ng, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.215 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.

Tortorici, M.A., Beltramello, M., Lempp, F.A., Pinto, D., Dang, H.V., Rosen, L.E., McCallum, M., Bowen, J., Minola, A., Jaconi, S., Zatta, F., De Marco, A., Guarino, B., Bianchi, S., Lauron, E.J., Tucker, H., Zhou, J., Peter, A., Havenar-Daughton, C., Wojcechowskyj, J.A., Case, J.B., Chen, R.E., Kaiser, H., Montiel-Ruiz, M., Meury, M., Czudnochowski, N., Spreafico, R., Dillen, J., Ng, C., Sprugasci, N., Culap, K., Benigni, F., Abdelnabi, R., Foo, S.C., Schmid, M.A., Cameroni, E., Riva, A., Gabrieli, A., Galli, M., Pizzuto, M.S., Neyts, J., Diamond, M.S., Virgin, H.W., Snell, G., Corti, D., Fink, K., Veesler, D.

(2020) Science 370: 950-957

• PubMed: 32972994 
• DOI: https://doi.org/10.1126/science.abe3354
• Primary Citation Related Structures: 
  7K3Q, 7K43, 7K45, 7K4N


• PubMed Abstract: 
  

  Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France.
Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
Vir Biotechnology, San Francisco, CA 94158, USA.
Departments of Medicine, Molecular Microbiology, Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium.
III Division of Infectious Diseases, Luigi Sacco University Hospital, University of Milan, Italy.
Washington University School of Medicine, St. Louis, MO, USA.
UTSouthwestern Medical Center, Dallas, TX, USA.
Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland. [e-mail] [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 47.75 kDa 
• Atom Count: 3,735 
• Modeled Residue Count: 442 
• Deposited Residue Count: 442 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of S2E12 monoclonal antibody, heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of S2E12 monoclonal antibody, light chain	B [auth L]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth H], E [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.215 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.014	α = 90
b = 85.722	β = 90
c = 86.306	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Snell, G., Czudnochowski, N., Ng, C.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary