7NLL

SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo.

Hanke, L.Das, H.Sheward, D.J.Perez Vidakovics, L.Urgard, E.Moliner-Morro, A.Kim, C.Karl, V.Pankow, A.Smith, N.L.Porebski, B.Fernandez-Capetillo, O.Sezgin, E.Pedersen, G.K.Coquet, J.M.Hallberg, B.M.Murrell, B.McInerney, G.M.

(2022) Nat Commun 13: 155-155

  • DOI: https://doi.org/10.1038/s41467-021-27610-z
  • Primary Citation of Related Structures:  
    7NLL, 7NS6

  • PubMed Abstract: 

    Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.


  • Organizational Affiliation

    Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1A [auth B],
B [auth D]
230Severe 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
Nanobody Fu2C [auth A],
D [auth C]
145Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.0.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 2.0: 2023-09-27
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Structure summary