8BSE

CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab

PDB DOI: https://doi.org/10.2210/pdb8BSE/pdb

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

Deposited: 2022-11-25 Released: 2023-05-17
Deposition Author(s): Welin, M., Kimbung, Y.R., Focht, D., Pisitkun, T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.

Boonkrai, C., Cotrone, T.S., Chaisuriyong, W., Tantawichien, T., Thisyakorn, U., Fernandez, S., Hunsawong, T., Reed, M., Wongtangprasert, T., Audomsun, T., Phakham, T., Attakitbancha, C., Saelao, P., Focht, D., Kimbung, R., Welin, M., Malik, A.A., Pisitkun, T., Srisawat, N.

(2023) PLoS One 18: e0284173-e0284173

PubMed: 37141227 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0284173
Primary Citation of Related Structures:
8BSE, 8BSF

PubMed Abstract:
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the biggest healthcare issue worldwide. This study aimed to develop a monoclonal antibody against SARS-CoV-2 from B cells of recovered COVID-19 patients, which might have beneficial therapeutic purposes for COVID-19 patients. We successfully generated human monoclonal antibodies (hmAbs) against the receptor binding domain (RBD) protein of SARS-CoV-2 using developed hybridoma technology. The isolated hmAbs against the RBD protein (wild-type) showed high binding activity and neutralized the interaction between the RBD and the cellular receptor angiotensin-converting enzyme 2 (ACE2) protein. Epitope binning and crystallography results displayed target epitopes of these antibodies in distinct regions beneficial in the mix as a cocktail. The 3D2 binds to conserved epitopes among multi-variants. Pseudovirion-based neutralization results revealed that the antibody cocktail, 1D1 and 3D2, showed high potency in multiple variants of SARS-CoV-2 infection. In vivo studies showed the ability of the antibody cocktail treatment (intraperitoneal (i.p.) administration) to reduce viral load (Beta variant) in blood and various tissues. While the antibody cocktail treatment (intranasal (i.n.) administration) could not significantly reduce the viral load in nasal turbinate and lung tissue, it could reduce the viral load in blood, kidney, and brain tissue. These findings revealed that the efficacy of the antibody cocktail, 1D1 and 3D2, should be further studied in animal models in terms of timing of administration, optimal dose, and efficacy to mitigate inflammation in targeted tissue such as nasal turbinate and lung.

Organizational Affiliation

Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, Thailand.

Macromolecule Content

Total Structure Weight: 73.67 kDa
Atom Count: 5,349
Modelled Residue Count: 619
Deposited Residue Count: 666
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	231	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1D1 FAB HEAVY CHAIN	B [auth H]	221	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1D1 FAB LIGHT CHAIN	C [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H]	I [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth H] SDF format, chain H SDF format, chain J [auth L] SDF format, chain G [auth H] MOL2 format, chain E [auth A] MOL2 format, chain F [auth H] MOL2 format, chain H MOL2 format, chain J [auth L] MOL2 format, chain G [auth H]	E [auth A], F [auth H], G [auth H], H, J [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain J [auth L] Interactions & Density Focus chain E [auth A] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain J [auth L]