7K9Z

Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

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This is version 1.2 of the entry. See complete history


Literature

Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.

Rujas, E.Kucharska, I.Tan, Y.Z.Benlekbir, S.Cui, H.Zhao, T.Wasney, G.A.Budylowski, P.Guvenc, F.Newton, J.C.Sicard, T.Semesi, A.Muthuraman, K.Nouanesengsy, A.Aschner, C.B.Prieto, K.Bueler, S.A.Youssef, S.Liao-Chan, S.Glanville, J.Christie-Holmes, N.Mubareka, S.Gray-Owen, S.D.Rubinstein, J.L.Treanor, B.Julien, J.P.

(2021) Nat Commun 12: 3661-3661

  • DOI: 10.1038/s41467-021-23825-2
  • Primary Citation of Related Structures:  
    7K9Z

  • PubMed Abstract: 
  • SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers ...

    SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC 50 ) values as low as 9 × 10 - 14 M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.


    Related Citations: 
    • Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers
      Rujas, E., Kucharska, I., Tan, Y.Z., Benlekbir, S., Cui, H., Zhao, T., Wasney, G., Budylowski, P., Guvenc, F., Newton, J.C., Sicard, T., Semesi, A., Muthuraman, K., Nouanesengsy, A., Prieto, K., Bueler, S.A., Youssef, S., Liao-Chan, S., Glanville, J., Christie-Holmes, N., Mubareka, S., Gray-Owen, S.D., Rubinstein, J.L., Treanor, B., Julien, J.P.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Department of Immunology, University of Toronto, Toronto, ON, Canada. jean-philippe.julien@sickkids.ca.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
52 Fab Heavy ChainA [auth H]220Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
52 Fab Light ChainB [auth L]215Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
298 Fab Light ChainC [auth A]220Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
298 Fab Heavy ChainD [auth B]222Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1E228Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
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Go to UniProtKB:  P0DTC2
Entity Groups  
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UniProt GroupP0DTC2
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.617α = 90
b = 87.617β = 90
c = 325.096γ = 120
Software Package:
Software NamePurpose
XPREPdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada6280100058
Canadian Institutes of Health Research (CIHR)CanadaPJ4-169662

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 1.2: 2021-07-28
    Changes: Database references