7B27

RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.266 

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
Surface glycoproteinA [auth AAA],
B [auth aba]
222Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for A0A6M6B9J6 (Severe acute respiratory syndrome coronavirus 2)
Explore A0A6M6B9J6 
Go to UniProtKB:  A0A6M6B9J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M6B9J6
Glycosylation
Glycosylation Sites: 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 NM1230C [auth CCC],
D [auth DDD]
141Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth aba]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.266 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.29α = 90
b = 63.29β = 90
c = 411.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyDFG For 2327

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: 2024-10-16
    Changes: Structure summary