SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2

  1. Claire M. Weekley
  2. Damian F. J. Purcell
  3. Michael W. Parker

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Abstract

Since SARS-CoV-2 emerged in 2019, genomic sequencing has identified mutations in the viral RNA including in the receptor-binding domain of the Spike protein. Structural characterisation of the Spike carrying point mutations aids in our understanding of how these mutations impact binding of the protein to its human receptor, ACE2, and to therapeutic antibodies. The Spike G485R mutation has been observed in multiple isolates of the virus and mutation of the adjacent residue E484 to lysine is known to contribute to antigenic escape. Here, we have crystallised the SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2. The crystal structure shows that while the G485 residue does not have a direct interaction with ACE2, its mutation to arginine affects the structure of the loop made by residues 480-488 in the receptor-binding motif, disrupting the interactions of neighbouring residues with ACE2 and with potential implications for antigenic escape from vaccines, antibodies and other biologics directed against SARS-CoV-2 Spike.

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    SciScore for 10.1101/2021.03.16.434488: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Plasmids: Residues 1-617 of human ACE2 ectodomain (UniProtKB Q9BYF1C) and SARS-CoV-2 spike residues 319-530 (GenBank QHD43416.1) with the G485R mutation, were each synthesised with a N-terminal honeybee melittin signal peptide and a C-terminal TEV protease cleavage site and His6-tag by GenScript (Hong Kong) and subcloned into the pFastBac1 vector.
    UniProtKB
    suggested: (UniProtKB, RRID:SCR_004426)
    Data were integrated using XDS and scaled with AIMLESS from the CCP4 program suite (Winn et al., 2011).
    CCP4
    suggested: (CCP4, RRID:SCR_007255)
    Molecular replacement was performed using Phaser from the Phenix program suite with the SARS-CoV-2 Spike RBD-ACE2 structure (PDB ID: 6LZG) used as a search model.
    Phenix
    suggested: (Phenix, RRID:SCR_014224)
    Alternate rounds of model building and refinement were performed using Coot (Emsley et al., 2010), REFMAC5 (Murshudov et al., 2011) and phenix.refine (Afonine et al., 2012).
    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2021.03.16.434488v1 on bioRxiv