Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2′- O -methyl transfer by SARS-CoV-2 nsp16

  1. George Minasov
  2. Monica Rosas-Lemus
  3. Ludmilla Shuvalova
  4. Nicole L. Inniss
  5. Joseph S. Brunzelle
  6. Courtney M. Daczkowski
  7. Paul Hoover
  8. Andrew D. Mesecar
  9. Karla J. F. Satchell

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Abstract

Efficient RNA capping by the SARS-CoV-2 methyltransferase requires metal ions and a unique four-residue insert.

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  1. Version published to 10.1126/scisignal.abh2071
  2. ScreenIT

    SciScore for 10.1101/2021.01.31.429023: (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
    The plot was created using GraphPad Prism V9 and shows the average and the standard deviation of three measurements using two different protein purifications.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The initial solutions went through several rounds of refinement in REFMAC v.
    REFMAC
    suggested: (Refmac, RRID:SCR_014225)
    5.8.0266 (31) and manual model corrections using Coot (32).
    Coot
    suggested: (Coot, RRID:SCR_014222)
    The quality control of the models during refinement and for the final validation of the structures were done using MolProbity (35) (http://molprobity.biochem.duke.edu/).
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)
    All models of the structures were created in PyMOL open source V 2.1 (36), diagram of interactions was created in LigPlot+ (37).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Structural, sequence alignment and phylogenic tree: The PDB coordinates of SARS-CoV-2 nsp16 and nsp10 were analyzed using the FATCAT (38), POSA (39) and DALI (40) servers to perform structural alignments with MERS-CoV, NS5, hCMTr1 and VP39.
    FATCAT
    suggested: (FATCAT, RRID:SCR_014631)
    The multiple sequence alignment was performed using Clustal-O (https://www.ebi.ac.uk/Tools/msa/clustalo/) and merged with the coordinates of the structure with PDB code 7JYY using ESPript 3.
    https://www.ebi.ac.uk/Tools/msa/clustalo/
    suggested: (Clustal Omega, RRID:SCR_001591)
    The phylogenic tree was created using MacVector and processed in iTol (https://itol.embl.de)
    MacVector
    suggested: (MacVector, RRID:SCR_015700)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 11 and 12. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    Results from scite Reference Check: We found one citation with an erratum. We recommend checking the erratum to confirm that it does not impact the accuracy of your citation.

    DOIStatusTitle
    10.1007/s40121-019-00260-xHas correctionInfectious Disease Management and Control with Povidone Iodi…

    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 10.1101/2021.01.31.429023v1 on bioRxiv