7NKT

RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies.

Wagner, T.R.Ostertag, E.Kaiser, P.D.Gramlich, M.Ruetalo, N.Junker, D.Haering, J.Traenkle, B.Becker, M.Dulovic, A.Schweizer, H.Nueske, S.Scholz, A.Zeck, A.Schenke-Layland, K.Nelde, A.Strengert, M.Walz, J.S.Zocher, G.Stehle, T.Schindler, M.Schneiderhan-Marra, N.Rothbauer, U.

(2021) EMBO Rep 22: e52325-e52325

  • DOI: https://doi.org/10.15252/embr.202052325
  • Primary Citation of Related Structures:  
    7B27, 7NKT

  • PubMed Abstract: 

    In light of the COVID-19 pandemic, there is an ongoing need for diagnostic tools to monitor the immune status of large patient cohorts and the effectiveness of vaccination campaigns. Here, we present 11 unique nanobodies (Nbs) specific for the SARS-CoV-2 spike receptor-binding domain (RBD), of which 8 Nbs potently inhibit the interaction of RBD with angiotensin-converting enzyme 2 (ACE2) as the major viral docking site. Following detailed epitope mapping and structural analysis, we select two inhibitory Nbs, one of which binds an epitope inside and one of which binds an epitope outside the RBD:ACE2 interface. Based on these, we generate a biparatopic nanobody (bipNb) with viral neutralization efficacy in the picomolar range. Using bipNb as a surrogate, we establish a competitive multiplex binding assay ("NeutrobodyPlex") for detailed analysis of the presence and performance of neutralizing RBD-binding antibodies in serum of convalescent or vaccinated patients. We demonstrate that NeutrobodyPlex enables high-throughput screening and detailed analysis of neutralizing immune responses in infected or vaccinated individuals, to monitor immune status or to guide vaccine design.


  • Organizational Affiliation

    Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1A [auth AAA]229Severe 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
neutralizing nanobody NM1226B [auth BBB]144Vicugna pacosMutation(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: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.093α = 90
b = 128.093β = 90
c = 77.676γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary