7VPY

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-022-03630-3
Primary Citation of 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.

Organizational Affiliation

Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan. maeda@cognano.co.jp.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	A, B	144	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.177
R-Value Observed: 0.179
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

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	--