2′-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography

  1. Mateusz Wilamowski
  2. Darren A. Sherrell
  3. George Minasov
  4. Youngchang Kim
  5. Ludmilla Shuvalova
  6. Alex Lavens
  7. Ryan Chard
  8. Natalia Maltseva
  9. Robert Jedrzejczak
  10. Monica Rosas-Lemus
  11. Nickolaus Saint
  12. Ian T. Foster
  13. Karolina Michalska
  14. Karla J. F. Satchell
  15. Andrzej Joachimiak

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Abstract

The 2′-O methyl group in Cap-1 is essential to protect viral RNA from host interferon-induced response. We determined crystal structures of SARS-CoV-2 Nsp10/16 heterodimer in complex with substrates (Cap-0 analog and S-adenosyl methionine) and products (Cap-1 analog and S-adenosyl-L-homocysteine) at room temperature using synchrotron serial crystallography. Analysis of these structures will aid structure-based drug design against 2′-O-methyltransferase from SARS-CoV-2.

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  1. Version published to 10.1073/pnas.2100170118
  2. Version published to 10.1101/2020.08.14.251421v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.08.14.251421: (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
    As new images are acquired, Globus Automate “flows” are launched to process them as follow: 1) moves new files from APS to Theta by using the Globus Transfer service 55; 2) performs DIALS stills_process 56 on batches of 256 images by using funcX 57, a function-as-a-service computation system (funcX uses Parsl 58 to abstract and acquire nodes on Theta as needed, and dispatches tasks to available nodes); 3) extracts metadata from files regarding identified diffractions, and generates visualizations (funcX) showing the locations of positive hits on the mesh; and 4) publishes raw data, metadata, and visualizations to a portal on the ALCF Petrel data system 59.
    Theta
    suggested: (THetA, RRID:SCR_001860)
    Successfully processed images with diffraction-produced integration files were returned to the beamline computers and later refined and merged using PRIME
    PRIME
    suggested: (Prime, RRID:SCR_014887)
    Structure solution and refinement: The crystal structures of the Nsp10/16 complex were solved by molecular replacement using MolRep 61 from the CCP4 package.
    CCP4
    suggested: (CCP4, RRID:SCR_007255)
    The structures were refined by multiple cycles in REFMAC v.
    REFMAC
    suggested: (Refmac, RRID:SCR_014225)
    5.8.0258 62 followed by manual edition of the model using Coot 63.
    Coot
    suggested: (Coot, RRID:SCR_014222)
    The stereochemistry of structures were analyzed using MolProbity and the Ramachandran plot.
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)
    Figures were prepared with PyMol and UCSF Chimera 64
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 34, 28 and 29. 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 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

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  4. Version published to 10.1101/2020.08.14.251421v1 on bioRxiv