8BSE | pdb_00008bse

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 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Models: experimental

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 
• DOI: https://doi.org/10.1371/journal.pone.0284173
• Primary Citation 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.
Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand.
Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.
Faculty of Medicine, Center of Excellence in Critical Care Nephrology, Chulalongkorn University, Bangkok, Thailand.
Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand.
Faculty of Medicine, Department of Medicine, Division of Infectious Diseases, Chulalongkorn University, Bangkok, Thailand.
The Excellence Chulalongkorn Comprehensive Cancer Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.
SARomics Biostructures AB, Medicon Village, Lund, Sweden.
Faculty of Medicine, Center of Excellence in Computational Molecular Biology, Chulalongkorn University, Bangkok, Thailand.
Faculty of Medicine, Department of Medicine, Division of Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.
Department of Critical Care Medicine, Center for Critical Care Nephrology, The CRISMA Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States of America.
Academy of Science, Royal Society of Thailand, Bangkok, Thailand.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1D1 FAB HEAVY CHAIN	B [auth H]	221	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1D1 FAB LIGHT CHAIN	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	I [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	E [auth A], F [auth H], G [auth H], H, J [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.216 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.177	α = 90
b = 110.018	β = 90
c = 149.392	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Welin, M., Kimbung, Y.R., Focht, D., Pisitkun, T.

---

Funding Organization	Location	Grant Number
Other government	Thailand	--

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.2: 2024-10-09
  Changes: Structure summary