7CAN | pdb_00007can

Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Receptor-binding domain (RBD)

• PDB DOI: https://doi.org/10.2210/pdb7CAN/pdb

• Classification: PROTEIN BINDING
• Organism(s): synthetic construct, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3), Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-06-09 Released: 2020-06-24 
• Deposition Author(s): Li, T., Yao, H., Cai, H., Qin, W., Li, D.
• Funding Organization(s): Chinese Academy of Sciences, National Science Foundation (NSF, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.267 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Models: experimental

Literature

A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection.

Li, T., Cai, H., Yao, H., Zhou, B., Zhang, N., van Vlissingen, M.F., Kuiken, T., Han, W., GeurtsvanKessel, C.H., Gong, Y., Zhao, Y., Shen, Q., Qin, W., Tian, X.X., Peng, C., Lai, Y., Wang, Y., Hutter, C.A.J., Kuo, S.M., Bao, J., Liu, C., Wang, Y., Richard, A.S., Raoul, H., Lan, J., Seeger, M.A., Cong, Y., Rockx, B., Wong, G., Bi, Y., Lavillette, D., Li, D.

(2021) Nat Commun 12: 4635-4635

• PubMed: 34330908 
• DOI: https://doi.org/10.1038/s41467-021-24905-z
• Primary Citation Related Structures: 
  7C8V, 7C8W, 7CAN


• PubMed Abstract: 
  

  SARS-CoV-2, the causative agent of COVID-19 ¹ , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein ^1-6 . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics ^7-17 . Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (K _D  = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC ₅₀  = 0.42 μg mL ^-1 ). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log ₁₀ . Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.

---

Organizational Affiliation: 
• State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China.
University of CAS, Beijing, China.
CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China.
Erasmus Laboratory Animal Science Center, Erasmus University Medical Center, Rotterdam, Netherlands.
European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France.
Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands.
National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China.
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China. [e-mail].
Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC, Canada. [e-mail].
University of CAS, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China. [e-mail].
CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China. [e-mail].
Pasteurien College, Soochow University, Jiangsu, China. [e-mail].
State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.98 kDa 
• Atom Count: 2,509 
• Modeled Residue Count: 312 
• Deposited Residue Count: 363 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sybody MR17-K99Y	A	150	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	213	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

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.267 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.191	α = 90
b = 74.191	β = 90
c = 158.404	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Li, T., Yao, H., Cai, H., Qin, W., Li, D.

---

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	QYZDB-SSW-SMC037, XDB37020204
National Science Foundation (NSF, China)	China	31870726

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-03-10
  Changes: Structure summary
• Version 2.2: 2022-01-05
  Changes: Database references
• Version 2.3: 2023-11-29
  Changes: Data collection, Refinement description
• Version 2.4: 2024-10-09
  Changes: Structure summary