7A25

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2.

Custodio, T.F.Das, H.Sheward, D.J.Hanke, L.Pazicky, S.Pieprzyk, J.Sorgenfrei, M.Schroer, M.A.Gruzinov, A.Y.Jeffries, C.M.Graewert, M.A.Svergun, D.I.Dobrev, N.Remans, K.Seeger, M.A.McInerney, G.M.Murrell, B.Hallberg, B.M.Low, C.

(2020) Nat Commun 11: 5588-5588

  • DOI: 10.1038/s41467-020-19204-y
  • Primary Citation of Related Structures:  
    7A29, 7A25

  • PubMed Abstract: 
  • The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development ...

    The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC 50 of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed an unusual conformation of the spike where two RBDs are in the 'up' ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.


    Related Citations: 
    • Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2
      Custodio, T.F., Das, H., Sheward, D.J., Hanke, L., Pazicky, S., Pieprzyk, J., Sorgenfrei, M., Schroer, M., Gruzinov, A., Jeffries, C., Graewert, M., Svergun, D., Dobrev, N., Remans, K., Seeger, M.A., McInerney, G.M., Murrell, B., Hallberg, B.M., Loew, C.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany. christian.loew@embl-hamburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinABC1146Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sybody 23DEF114synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, Q, U, b, d, f, t, v, y
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-11-25
    Type: Initial release