8XK2

A neutralizing nanobody VHH60 against wt SARS-CoV-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41419-024-06802-7
  • Primary Citation of 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.


  • Organizational Affiliation

    State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1
A, C, E, G
219Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VHH60 nanobody
B, D, F, H
121synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.85α = 90
b = 100.61β = 90
c = 227.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPXdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government92169109
Other governmentZD2021CY001

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release