7QF1 | pdb_00007qf1

Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264

• PDB DOI: https://doi.org/10.2210/pdb7QF1/pdb

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


• Deposited: 2021-12-03 Released: 2022-05-18 
• Deposition Author(s): Fernandez, I., Pederzoli, R., Rey, F.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.254 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Models: experimental

Literature

Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.

Planchais, C., Fernandez, I., Bruel, T., de Melo, G.D., Prot, M., Beretta, M., Guardado-Calvo, P., Dufloo, J., Molinos-Albert, L.M., Backovic, M., Chiaravalli, J., Giraud, E., Vesin, B., Conquet, L., Grzelak, L., Planas, D., Staropoli, I., Guivel-Benhassine, F., Hieu, T., Boulle, M., Cervantes-Gonzalez, M., Ungeheuer, M.N., Charneau, P., van der Werf, S., Agou, F., Dimitrov, J.D., Simon-Loriere, E., Bourhy, H., Montagutelli, X., Rey, F.A., Schwartz, O., Mouquet, H.

(2022) J Exp Medicine 219

• PubMed: 35704748 
• DOI: https://doi.org/10.1084/jem.20220638
• Primary Citation Related Structures: 
  7QEZ, 7QF0, 7QF1


• PubMed Abstract: 
  

  Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in Wuhan COVID-19 convalescents combining serological, cellular, and monoclonal antibody explorations revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor-binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.

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Organizational Affiliation: 
• Institut Pasteur, Université Paris Cité, Laboratory of Humoral Immunology, Paris, France.
INSERM U1222, Paris, France.
Institut Pasteur, Université Paris Cité, Structural Virology Unit, Paris, France.
CNRS UMR3569, Paris, France.
Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France.
Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France.
Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France.
Institut Pasteur, Université Paris Cité, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France.
Pasteur-TheraVectys, Paris, France.
Institut Pasteur, Université Paris Cité, Molecular Virology & Vaccinology Unit, Paris, France.
Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, Paris, France.
Institut Pasteur, Université Paris Cité, Functional Genetics of Infectious Diseases Unit, Paris, France.
Department of Epidemiology, Biostatistics and Clinical Research, Assistance Publique-Hôpitaux de Paris, Bichat Claude Bernard University Hospital, INSERM CIC-EC 1425, Paris, France.
Institut Pasteur, Université Paris Cité, Investigation Clinique et Accès aux Ressources Biologiques, Center for Translational Research, Paris, France.
Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, Paris, France.
Université de Paris, Paris, France.
Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 144.14 kDa 
• Atom Count: 9,689 
• Modeled Residue Count: 1,248 
• Deposited Residue Count: 1,310 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B [auth F]	206	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CV2.6264 light chain	C [auth B], E [auth D]	213	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CV2.6264 heavy chain	D [auth C], F [auth E]	236	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.254 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.163	α = 90
b = 191.319	β = 90
c = 220.928	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Fernandez, I., Pederzoli, R., Rey, F.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2023-06-28
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary