7VPY | pdb_00007vpy

Crystal structure of the neutralizing nanobody P86 against SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb7VPY/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Vicugna pacos
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-18 Released: 2022-07-20 
• Deposition Author(s): Maeda, R., Fujita, J., Konishi, Y., Kazuma, Y., Yamazaki, H., Anzai, I., Yamaguchi, K., Kasai, K., Nagata, K., Yamaoka, Y., Miyakawa, K., Ryo, A., Shirakawa, K., Makino, F., Matsuura, Y., Inoue, T., Imura, A., Namba, K., Takaori-Kondo, A.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.

Maeda, R., Fujita, J., Konishi, Y., Kazuma, Y., Yamazaki, H., Anzai, I., Watanabe, T., Yamaguchi, K., Kasai, K., Nagata, K., Yamaoka, Y., Miyakawa, K., Ryo, A., Shirakawa, K., Sato, K., Makino, F., Matsuura, Y., Inoue, T., Imura, A., Namba, K., Takaori-Kondo, A.

(2022) Commun Biol 5: 669-669

• PubMed: 35794202 
• DOI: https://doi.org/10.1038/s42003-022-03630-3
• Primary Citation Related Structures: 
  7VPY, 7VQ0


• PubMed Abstract: 
  

  We are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, and those in war crises, have been problematic. Nanobodies are small, stable, customizable, and inexpensive to produce. Herein, we present a panel of nanobodies that can detect the spike proteins of five SARS-CoV-2 variants of concern (VOCs) including Omicron. Here we show via ELISA, lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays that our nanobodies can quantify the spike variants. This panel of nanobodies broadly neutralizes viral infection caused by pseudotyped and authentic SARS-CoV-2 VOCs. Structural analyses show that the P86 clone targets epitopes that are conserved yet unclassified on the receptor-binding domain (RBD) and contacts the N-terminal domain (NTD). Human antibodies rarely access both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins that go undetected by conventional antibodies.

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Organizational Affiliation: 
• Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan. [e-mail].
COGNANO Inc., Kyoto, 601-1255, Japan. [e-mail].
Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan.
Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
COGNANO Inc., Kyoto, 601-1255, Japan.
Shizuoka City Shizuoka Hospital, Shizuoka, 420-8630, Japan.
Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan.
Department of Microbiology and Molecular Biodefense Research, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
Division of System Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
CREST, Japan Science and Technology Agency, Saitama, 332-0012, Japan.
JEOL Ltd., Tokyo, 196-8558, Japan.
Centre for Infectious Disease Education and Research, Osaka University, Osaka, 565-0871, Japan.
Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan.
COGNANO Inc., Kyoto, 601-1255, Japan. [e-mail].
Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan. [e-mail].
JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Osaka, 565-0871, Japan. [e-mail].
RIKEN Centre for Biosystems Dynamics Research and SPring-8 Centre, Osaka, 565-0871, Japan. [e-mail].
Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.22 kDa 
• Atom Count: 2,167 
• Modeled Residue Count: 232 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	A, B	144	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.078	α = 90
b = 43.166	β = 110.758
c = 56.027	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Maeda, R., Fujita, J., Konishi, Y., Kazuma, Y., Yamazaki, H., Anzai, I., Yamaguchi, K., Kasai, K., Nagata, K., Yamaoka, Y., Miyakawa, K., Ryo, A., Shirakawa, K., Makino, F., Matsuura, Y., Inoue, T., Imura, A., Namba, K., Takaori-Kondo, A.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	20fk0108268
Japan Agency for Medical Research and Development (AMED)	Japan	20fk018517
Japan Agency for Medical Research and Development (AMED)	Japan	20fk018413
Japan Science and Technology	Japan	--
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary