Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus

  1. Qi Peng
  2. Ruchao Peng
  3. Bin Yuan
  4. Jingru Zhao
  5. Min Wang
  6. Xixi Wang
  7. Qian Wang
  8. Yan Sun
  9. Zheng Fan
  10. Jianxun Qi
  11. George F. Gao
  12. Yi Shi

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Abstract

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus. The viral polymerase is a promising antiviral target. However, the structure of COVID-19 virus polymerase is yet unknown. Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate a well adaptation of COVID-19 virus towards humans with relatively lower body temperatures than the natural bat hosts.

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    SciScore for 10.1101/2020.04.23.057265: (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

    Software and Algorithms
    SentencesResources
    The data was automatically collected using SerialEM software (http://bio3d.colorado.edu/SerialEM/).
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    Image processing: The image drift and anisotropic magnification was corrected using MotionCor2 (Zheng et al., 2017).
    MotionCor2
    suggested: (MotionCor2, RRID:SCR_016499)
    The model was manually corrected for local fit in COOT (Emsley et al., 2010) and the sequence register was corrected based on alignment.
    COOT
    suggested: (Coot, RRID:SCR_014222)
    The initial model was refined in real space using PHENIX (Adams et al., 2010) with the secondary structural restraints and Ramachandran restrains applied.
    PHENIX
    suggested: (Phenix, RRID:SCR_014224)
    The model was further adjusted and refined iteratively for several rounds aided by the stereochemical quality assessment using MolProbity (Chen et al., 2010).
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)
    Structural figures were rendered by either CHIMERA (Pettersen et al., 2004) or PyMOL (https://pymol.org/).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Images were taken using a Vilber Fusion system and analyzed with the Image J software.
    Image J
    suggested: (ImageJ, RRID:SCR_003070)

    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 page 30. 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.

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  2. Version published to 10.1101/2020.04.23.057265 on bioRxiv