Distinct conformational states of SARS-CoV-2 spike protein

  1. Yongfei Cai
  2. Jun Zhang
  3. Tianshu Xiao
  4. Hanqin Peng
  5. Sarah M. Sterling
  6. Richard M. Walsh
  7. Shaun Rawson
  8. Sophia Rits-Volloch
  9. Bing Chen

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Abstract

Efforts to protect human cells against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have focused on the trimeric spike (S) protein. Several structures have shown a stabilized ectodomain of the spike in its prefusion conformation. Cai et al. now provide insight into the structural changes in the S protein that result in the fusion of the viral and host cell membranes. They purified full-length S protein and determined cryo–electron microscopy structures of both the prefusion and postfusion conformations. These structures add to our understanding of S protein function and could inform vaccine design.

Science , this issue p. 1586

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  1. Version published to 10.1126/science.abd4251
  2. ScreenIT

    SciScore for 10.1101/2020.05.16.099317: (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.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Western blot: Western blot was performed either using an anti-strep tag antibody or anti-SARA-COV-2 S antibody following a protocol described previously50.
    anti-SARA-COV-2 S
    suggested: None
    Membranes were blocked with 5% skimmed milk in PBS for 1 hour and incubated either with anti-strep tag antibody (IBA Lifesciences) or anti-SARS-COV-2 polyclone antibody (Sino Biological Inc.) for another hour at room temperature.
    anti-strep tag
    suggested: None
    anti-SARS-COV-2
    suggested: None
    Alkaline phosphatase conjugated anti-Rabbit IgG (1:5000) (Sigma) was used as a secondary antibody.
    anti-Rabbit IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Varying amount of the full-length SARS-CoV2 S protein expression construct (0.1-10 µg) and the α fragment of β-galactosidase construct (10 µg), or the full-length ACE2 expression construct (10 µg) together with the ω fragment of β-galactosidase construct (10 µg), were mixed with DMEM medium (Gibco) containing PEI (80 µg) and added to HEK293T cells.
    HEK293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    Software and Algorithms
    SentencesResources
    Automated data collection was carried out using SerialEM version65 at a magnification of 105,000× and the K3 detector in counting mode (pixel size, 0.825 Å) at a dose rate of ∼1.1 electrons per physical pixels per second.
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    For the S1 fragment data set, CrYOLO53 was used for particle picking, RELION 3.0.8 was used for 2D classification, 3D classification and refinement.
    RELION
    suggested: (RELION, RRID:SCR_016274)
    Structural biology applications used in this project were compiled and configured by SBGrid56 Model building: The initial templates for model building used the stabilized SARS-CoV-2 S ectodomain trimer structure (PDB ID 6vxx) for the prefusion conformation, and a homology model, calculated by I-TASSER, of S2 postfusion trimer structure from mouse hepatitis virus (MHV) (PDB ID: 6b3o) for the postfusion confirmation.
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    Several rounds of manual building were performed in Coot.
    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 26 and 23. 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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  3. Version published to 10.1101/2020.05.16.099317v1 on bioRxiv