Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV ‐2

  1. Youngchang Kim
  2. Robert Jedrzejczak
  3. Natalia I. Maltseva
  4. Mateusz Wilamowski
  5. Michael Endres
  6. Adam Godzik
  7. Karolina Michalska
  8. Andrzej Joachimiak

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Abstract

Severe Acute Respiratory Syndrome coronavirus 2 (SARS‐CoV‐2) is rapidly spreading around the world. There is no existing vaccine or proven drug to prevent infections and stop virus proliferation. Although this virus is similar to human and animal SARS‐CoVs and Middle East Respiratory Syndrome coronavirus (MERS‐CoVs), the detailed information about SARS‐CoV‐2 proteins structures and functions is urgently needed to rapidly develop effective vaccines, antibodies, and antivirals. We applied high‐throughput protein production and structure determination pipeline at the Center for Structural Genomics of Infectious Diseases to produce SARS‐CoV‐2 proteins and structures. Here we report two high‐resolution crystal structures of endoribonuclease Nsp15/NendoU. We compare these structures with previously reported homologs from SARS and MERS coronaviruses.

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    SciScore for 10.1101/2020.03.02.968388: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.RandomizationRfree is calculated analogously for the test reflections, randomly selected and excluded from the refinement. d As defined by Molprobity (Davis et al., 2004) Figures Figure 1.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Although this virus is similar to human and animal SARS- and MERS-CoVs the detailed information about SARSCoV-2 proteins structures and functions is urgently needed to rapidly develop effective vaccines, antibodies and antivirals.
    antivirals
    suggested: None
    Software and Algorithms
    SentencesResources
    Intensities were converted to structure factor amplitudes in the Ctruncate program ( French & Wilson , 1978 , Padilla & Yeates , 2003 ) from the CCP4 package ( Winn et al. , 2011) .
    CCP4
    suggested: (CCP4, SCR_007255)
    The initial solution was manually adjusted using COOT ( Emsley & Cowtan , 2004 ) and then iteratively refined using COOT , PHENIX ( Adams et al. , 2010 ) and REFMAC ( Murshudov et al. , 1997 , Winn et al. , 2011) .
    COOT
    suggested: (Coot, SCR_014222)
    Initially REFMAC refinement worked better for the structure which was subsequently moved to PHENIX to finalize the refinement .
    PHENIX
    suggested: (Phenix, SCR_014224)
    Throughout the refinement , the same 5 % of reflections were kept out throughout from the refinement ( in both REFMAC and PHENIX refinement) .
    REFMAC
    suggested: (Refmac, SCR_014225)
    Rfree is calculated analogously for the test reflections, randomly selected and excluded from the refinement. d As defined by Molprobity (Davis et al., 2004) Figures Figure 1.
    Molprobity
    suggested: (MolProbity, SCR_014226)

    Results from OddPub: Thank you for sharing your data.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  2. Version published to 10.1002/pro.3873
  3. Version published to 10.1101/2020.03.02.968388v1 on bioRxiv