7P40 | pdb_00007p40

P5C3 is a potent fab neutralizer

• PDB DOI: https://doi.org/10.2210/pdb7P40/pdb
• Entry: 7P40 supersedes: 7NY5
• EM Map EMD-13190: EMDB EMDataResource

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


• Deposited: 2021-07-09 Released: 2021-10-13 
• Deposition Author(s): perez, L.

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Experimental Data Snapshot

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

Starting Model: experimental

Literature

A highly potent antibody effective against SARS-CoV-2 variants of concern.

Fenwick, C., Turelli, P., Perez, L., Pellaton, C., Esteves-Leuenberger, L., Farina, A., Campos, J., Lana, E., Fiscalini, F., Raclot, C., Pojer, F., Lau, K., Demurtas, D., Descatoire, M., Joo, V.S., Foglierini, M., Noto, A., Abdelnabi, R., Foo, C.S., Vangeel, L., Neyts, J., Du, W., Bosch, B.J., Veldman, G., Leyssen, P., Thiel, V., LeGrand, R., Levy, Y., Trono, D., Pantaleo, G.

(2021) Cell Rep 37: 109814-109814

• PubMed: 34599871 
• DOI: https://doi.org/10.1016/j.celrep.2021.109814
• Primary Citation Related Structures: 
  7P40, 7PHG


• PubMed Abstract: 
  

  Control of the ongoing SARS-CoV-2 pandemic is endangered by the emergence of viral variants with increased transmission efficiency, resistance to marketed therapeutic antibodies, and reduced sensitivity to vaccine-induced immunity. Here, we screen B cells from COVID-19 donors and identify P5C3, a highly potent and broadly neutralizing monoclonal antibody with picomolar neutralizing activity against all SARS-CoV-2 variants of concern (VOCs) identified to date. Structural characterization of P5C3 Fab in complex with the spike demonstrates a neutralizing activity defined by a large buried surface area, highly overlapping with the receptor-binding domain (RBD) surface necessary for ACE2 interaction. We further demonstrate that P5C3 shows complete prophylactic protection in the SARS-CoV-2-infected hamster challenge model. These results indicate that P5C3 opens exciting perspectives either as a prophylactic agent in immunocompromised individuals with poor response to vaccination or as combination therapy in SARS-CoV-2-infected individuals.

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Organizational Affiliation: 
• Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium.
Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
Abbvie Bioresearch Center, Worcester, MA, USA.
Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France.
VRI, Université Paris-Est Créteil, Faculté de Médicine, INSERM U955, 94010 Créteil, France; INSERM U955, Equipe 16, Créteil, France; AP-HP, Ho^pital Henri-Mondor Albert-Chenevier, Service d'Immunologie Clinique et Maladies Infectieuses, Créteil, France.
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. Electronic address: [e-mail].
Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; VRI, Université Paris-Est Créteil, Faculté de Médicine, INSERM U955, 94010 Créteil, France; Swiss Vaccine Research Institute, Lausanne University Hospital and University of Lausanne, Switzerland. Electronic address: [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.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 564.94 kDa 
• Atom Count: 26,466 
• Modeled Residue Count: 3,687 
• Deposited Residue Count: 5,151 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, E, G	1,281	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Light Chain P5C3 (VL)	B, D, H	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Heavy Chain P5C3 (VH)	C, F, I	221	Homo sapiens	Mutation(s): 0

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	Coot
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): perez, L.
• This entry supersedes: 7NY5

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2021-10-27
  Changes: Data collection, Database references
• Version 1.2: 2023-04-12
  Changes: Advisory, Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary