7Y3O | pdb_00007y3o

Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56

• PDB DOI: https://doi.org/10.2210/pdb7Y3O/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-06-11 Released: 2023-12-27 
• Deposition Author(s): Rao, X., Gao, F., Wu, Y., Gao, F.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Models: experimental

Literature

Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.

Rao, X., Zhao, R., Tong, Z., Guo, S., Peng, W., Liu, K., Li, S., Wu, L., Tong, J., Chai, Y., Han, P., Wang, F., Jia, P., Li, Z., Zhao, X., Li, D., Zhang, R., Zhang, X., Zou, W., Li, W., Wang, Q., Gao, G.F., Wu, Y., Dai, L., Gao, F.

(2023) Proc Natl Acad Sci U S A 120: e2314193120-e2314193120

• PubMed: 38109549 
• DOI: https://doi.org/10.1073/pnas.2314193120
• Primary Citation Related Structures: 
  7Y3N, 7Y3O, 8HRD


• PubMed Abstract: 
  

  Currently, monoclonal antibodies (MAbs) targeting the SARS-CoV-2 receptor binding domain (RBD) of spike (S) protein are classified into seven classes based on their binding epitopes. However, most of these antibodies are seriously impaired by SARS-CoV-2 Omicron and its subvariants, especially the recent BQ.1.1, XBB and its derivatives. Identification of broadly neutralizing MAbs against currently circulating variants is imperative. In this study, we identified a "breathing" cryptic epitope in the S protein, named as RBD-8. Two human MAbs, BIOLS56 and IMCAS74, were isolated recognizing this epitope with broad neutralization abilities against tested sarbecoviruses, including SARS-CoV, pangolin-origin coronaviruses, and all the SARS-CoV-2 variants tested (Omicron BA.4/BA.5, BQ.1.1, and XBB subvariants). Searching through the literature, some more RBD-8 MAbs were defined. More importantly, BIOLS56 rescues the immune-evaded antibody, RBD-5 MAb IMCAS-L4.65, by making a bispecific MAb, to neutralize BQ.1 and BQ.1.1, thereby producing an MAb to cover all the currently circulating Omicron subvariants. Structural analysis reveals that the neutralization effect of RBD-8 antibodies depends on the extent of epitope exposure, which is affected by the angle of antibody binding and the number of up-RBDs induced by angiotensin-converting enzyme 2 binding. This cryptic epitope which recognizes non- receptor binding motif (non-RBM) provides guidance for the development of universal therapeutic antibodies and vaccines against COVID-19.

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Organizational Affiliation: 
• Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Institute of Physical Science and Information, Anhui University, Hefei 230039, China.
Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China.
Faculty of Health Sciences, University of Macau, Macau Special Administrative Region 999078, China.
Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518038, China.
School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.
Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China.
Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.49 kDa 
• Atom Count: 5,493 
• Modeled Residue Count: 634 
• Deposited Residue Count: 634 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of BIOLS56	A [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of BIOLS56	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth A]	194	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

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.23	α = 90
b = 74.839	β = 90
c = 214.499	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Rao, X., Gao, F., Wu, Y., Gao, F.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB29010202

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description