Structure of a germline-like human antibody defines a neutralizing epitope on the SARS-CoV-2 spike NTD

  1. Clara G. Altomare
  2. Daniel C. Adelsberg
  3. Juan Manuel Carreno
  4. Iden A. Sapse
  5. Fatima Amanat
  6. Ali H. Ellebedy
  7. Viviana Simon
  8. Florian Krammer
  9. Goran Bajic

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Abstract

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germline-like monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against SARS-CoV-2 and determined its structure in complex with the spike glycoprotein by cryo-EM. We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its HCDR3 loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that - because of the conserved nature of the epitope – the mAb maintains binding to viral variants B.1.1.7 and B.1.351. Our study illustrates the feasibility of targeting the NTD to achieve broad neutralization against SARS-CoV-2 variants.

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  1. ScreenIT

    SciScore for 10.1101/2021.07.08.451649: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Anti-human IgG-Biotin (Abcam) in PBS-T was added to each and incubated for 1hr at RT.
    Anti-human IgG-Biotin
    suggested: None
    After 24 hours, cells were permeabilized and stained using an anti-nucleoprotein antibody 1C7 as discussed in detail earlier37,43.
    anti-nucleoprotein
    suggested: None
    Recombinant DNA
    SentencesResources
    Spike proteins for enzyme-linked immunosorbent assay (ELISA) were cloned into a mammalian expression vector, pCAGGS as described earlier37,38 and purified after transient transfections with each respective plasmid.
    pCAGGS
    suggested: RRID:Addgene_18926)
    Software and Algorithms
    SentencesResources
    Data were plotted in Prism 9 (GraphPad Software) and area under the curve (AUC) calculated.
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Serial dilutions of the mAb samples were made in 1X minimal essential medium (MEM; Life Technologies) starting at 30 µg/ml.
    MEM
    suggested: (E-mem, RRID:SCR_016081)
    For the remainder of the spike, a previously published structure (PDB ID 7NTC) was docked into the sharpened full map in UCSF Chimera then manually fit in COOT.
    COOT
    suggested: (Coot, RRID:SCR_014222)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.07.08.451649v1 on bioRxiv