8XK2 | pdb_00008xk2

A neutralizing nanobody VHH60 against wt SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8XK2/pdb

• Classification: ANTIVIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-22 Released: 2024-07-10 
• Deposition Author(s): Lu, Y., Guo, H., Ji, X., Yang, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.300 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Models: experimental, in silico

Literature

A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug.

Liu, Q., Lu, Y., Cai, C., Huang, Y., Zhou, L., Guan, Y., Fu, S., Lin, Y., Yan, H., Zhang, Z., Li, X., Yang, X., Yang, H., Guo, H., Lan, K., Chen, Y., Hou, S.C., Xiong, Y.

(2024) Cell Death Dis 15: 458-458

• PubMed: 38937437 
• DOI: https://doi.org/10.1038/s41419-024-06802-7
• Primary Citation Related Structures: 
  8XK2, 8XKI


• PubMed Abstract: 
  

  SARS-CoV-2 infection is initiated by Spike glycoprotein binding to the human angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain. Blocking this interaction has been proven to be an effective approach to inhibit virus infection. Here we report the discovery of a neutralizing nanobody named VHH60, which was directly produced from an engineering nanobody library based on a commercialized nanobody within a very short period. VHH60 competes with human ACE2 to bind the receptor binding domain of the Spike protein at S ³⁵¹ , S ^470-471 and S ^493-494 as determined by structural analysis, with an affinity of 2.56 nM. It inhibits infections of both ancestral SARS-CoV-2 strain and pseudotyped viruses harboring SARS-CoV-2 wildtype, key mutations or variants at the nanomolar level. Furthermore, VHH60 suppressed SARS-CoV-2 infection and propagation 50-fold better and protected mice from death for twice as long as the control group after SARS-CoV-2 nasal infections in vivo. Therefore, VHH60 is not only a powerful nanobody with a promising profile for disease control but also provides evidence for a highly effective and rapid approach to generating therapeutic nanobodies.

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Organizational Affiliation: 
• State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
Lingang Laboratory, Shanghai, 200031, China.
Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China.
State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
Animal Biosafety Level-III Laboratory/Institute for Vaccine Research, Wuhan University, Wuhan, 430071, China.
The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China. [e-mail].
State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China. [e-mail].
Animal Biosafety Level-III Laboratory/Institute for Vaccine Research, Wuhan University, Wuhan, 430071, China. [e-mail].
State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China. [e-mail].
State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China. [e-mail].
Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China. [e-mail].
State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China. [e-mail].
Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China. [e-mail].
Bayray Innovation Center, Shenzhen Bay Laboratory, Shenzhen, 518107, Guangdong, 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 152.4 kDa 
• Atom Count: 9,406 
• Modeled Residue Count: 1,202 
• Deposited Residue Count: 1,360 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, C, E, G	219	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH60 nanobody	B, D, F, H	121	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.300 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.85	α = 90
b = 100.61	β = 90
c = 227.43	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Lu, Y., Guo, H., Ji, X., Yang, H.

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Funding Organization	Location	Grant Number
Other government		92169109
Other government		ZD2021CY001

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary