Structural insights into the cross-neutralization of SARS-CoV and SARS-CoV-2 by the human monoclonal antibody 47D11

  1. Juliette Fedry
  2. Daniel L. Hurdiss
  3. Chunyan Wang
  4. Wentao Li
  5. Gonzalo Obal
  6. Ieva Drulyte
  7. Wenjuan Du
  8. Stuart C. Howes
  9. Frank J.M. van Kuppeveld
  10. Friedrich Förster
  11. Berend-Jan Bosch

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Abstract

Cryo-EM reveals the molecular basis of SARS-CoV-2 cross-neutralization by the monoclonal antibody 47D11.

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  1. Version published to 10.1126/sciadv.abf5632
  2. ScreenIT

    SciScore for 10.1101/2020.09.30.318261: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    Plates were washed three times and incubated with horseradish peroxidase (HRP)-conjugated goat anti-human secondary antibody (ITK Southern Biotech) diluted 1:2000 in blocking buffer for 1 hour at RT.
    anti-human secondary antibody (ITK
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    HEK-293T cells were transfected with pCAGGS expression vectors encoding SARS2-S carrying a 18-a.a. cytoplasmic tail truncation, respectively.
    HEK-293T
    suggested: None
    Software and Algorithms
    SentencesResources
    The half maximal inhibitory concentration (IC50) was determined using 4-parameter logistic regression (GraphPad Prism version 8).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Half-maximum effective concentration (EC50) binding values were calculated by non-linear regression analysis on the binding curves using GraphPad Prism (version 8).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Cryo-EM data processing: Single-particle analysis was performed in Relion version 3.1.(52).
    Relion
    suggested: (RELION, RRID:SCR_016274)
    Drift and gain correction were performed with MotionCor2(53), CTF parameters were estimated using CTFFind4(54) and particles were picked using the Laplacian picker in Relion(52).
    MotionCor2
    suggested: (MotionCor2, RRID:SCR_016499)
    Model building and refinement: UCSF Chimera (version 1.12.0) and Coot (version, 1.0.) were used for model building and analysis(55, 56).
    Coot
    suggested: (Coot, RRID:SCR_014222)
    Phenix sculptor was used to create an initial model for the Fab chains(60), removing the non-aligning regions (notably the CDRH3).
    Phenix
    suggested: (Phenix, RRID:SCR_014224)
    Models were refined against the respective EM density maps using Phenix Real Space Refinement and Isolde(61)(62), and validated with MolProbity and Privateer (glycans)(63–65).
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

    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.

  3. Version published to 10.1101/2020.09.30.318261v2 on bioRxiv
  4. Version published to 10.1101/2020.09.30.318261v1 on bioRxiv