7YCO | pdb_00007yco

Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody

• PDB DOI: https://doi.org/10.2210/pdb7YCO/pdb

• Classification: PROTEIN BINDING
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Cyclostomatida
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-01 Released: 2023-07-05 
• Deposition Author(s): Kim, U.J., Cho, H.S.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

A bivalent form of a RBD-specific synthetic antibody effectively neutralizes SARS-CoV-2 variants.

Kim, D.G., Kim, U., Park, I.H., Ryu, B., Yoo, Y., Cha, J.S., Yoon, G.Y., Kim, S.H., Oh, H., Seo, J.Y., Nam, K.T., Seong, J.K., Shin, J.S., Cho, H.S., Kim, H.S.

(2023) Antiviral Res 220: 105738-105738

• PubMed: 37944822 
• DOI: https://doi.org/10.1016/j.antiviral.2023.105738
• Primary Citation Related Structures: 
  7YCO, 8H6F


• PubMed Abstract: 
  

  Coronavirus Disease 2019 (COVID-19) pandemic is severely impacting the world, and tremendous efforts have been made to deal with it. Despite many advances in vaccines and therapeutics, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains an intractable challenge. We present a bivalent Receptor Binding Domain (RBD)-specific synthetic antibody, specific for the RBD of wild-type (lineage A), developed from a non-antibody protein scaffold composed of LRR (Leucine-rich repeat) modules through phage display. We further reinforced the unique feature of the synthetic antibody by constructing a tandem dimeric form. The resulting bivalent form showed a broader neutralizing activity against the variants. The in vivo neutralizing efficacy of the bivalent synthetic antibody was confirmed using a human ACE2-expressing mouse model that significantly alleviated viral titer and lung infection. The present approach can be used to develop a synthetic antibody showing a broader neutralizing activity against a multitude of SARS-CoV-2 variants.

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Organizational Affiliation: 
• Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea.
Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, South Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea.
Institute for Basic Science (IBS), Daejeon, 34126, South Korea.
Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
Korea Mouse Phenotyping Center, Seoul National University, Seoul, 08826, South Korea.
Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, South Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, South Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea; Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea. Electronic address: [e-mail].
Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea. Electronic address: [e-mail].
Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 52.62 kDa 
• Atom Count: 3,757 
• Modeled Residue Count: 456 
• Deposited Residue Count: 465 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	198	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
Repebody (A6)	B	267	Cyclostomatida	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.966	α = 90
b = 135.966	β = 90
c = 69.556	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Kim, U.J., Cho, H.S.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C3010506
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019M3E5D6063903

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary
• Version 1.2: 2026-09-09
  Changes: Database references