7TPR

Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-CoV-2 variants


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Camel nanobodies broadly neutralize SARS-CoV-2 variants

Hong, J.Kwon, H.J.Cachau, R.Chen, C.Z.Dandey, V.P.Martin, N.Esposito, D.Ortega-Rodriguez, U.Xu, M.Borgnia, M.J.Xie, H.Ho, M.

(2021) bioRxiv 

  • DOI: https://doi.org/10.1101/2021.10.27.465996
  • Primary Citation of Related Structures:  
    7TPR

  • PubMed Abstract: 

    With the emergence of SARS-CoV-2 variants, there is urgent need to develop broadly neutralizing antibodies. Here, we isolate two V H H nanobodies (7A3 and 8A2) from dromedary camels by phage display, which have high affinity for the receptor-binding domain (RBD) and broad neutralization activities against SARS-CoV-2 and its emerging variants. Cryo-EM complex structures reveal that 8A2 binds the RBD in its up mode and 7A3 inhibits receptor binding by uniquely targeting a highly conserved and deeply buried site in the spike regardless of the RBD conformational state. 7A3 at a dose of ≥5 mg/kg efficiently protects K18-hACE2 transgenic mice from the lethal challenge of B.1.351 or B.1.617.2, suggesting that the nanobody has promising therapeutic potentials to curb the COVID-19 surge with emerging SARS-CoV-2 variants. Dromedary camel ( Camelus dromedarius ) V H H phage libraries were built for isolation of the nanobodies that broadly neutralize SARS-CoV-2 variants.


  • Organizational Affiliation

    Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health; Bethesda, Maryland, 20891, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,145Severe acute respiratory syndrome coronavirus 2Mutation(s): 9 
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
Nanobody 8A2
D, E
132Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 7A3
F, G, H
125Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA ES 103341
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesZIA BC 011943
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIC ES 10326
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesZIC BC 011891
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesZ01 BC010891
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesZIA BC010891
National Institutes of Health/National Cancer Institute (NIH/NCI)United States75N91019D00024

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary