Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

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1. Version published to 10.1126/sciadv.abe5575

   Jan 1, 2021
2. 

   ScreenIT

   Jul 2, 2020

   SciScore for 10.1101/2020.06.30.177097: (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

   Antibodies
   Sentences	Resources
   Anti-RBD polyclonal antibody and monoclonal antibody (MAb) 1A10 were prepared by immunizing BALB/c mice with recombinant SARS-CoV-2 RBD fused with a C-terminal mouse IgGFc tag (Sino Biological Inc, Beijing, China) using previously described protocols (Qu et al., 2020).	Anti-RBD suggested: None
   After washing, the corresponding secondary antibodies, horseradish peroxidase (HRP)-conjugated anti-human IgG1 (Abcam, USA) or HRP-conjugated anti-mouse IgG (Sigma, USA), were added and incubated at 37°C for 1 h.	anti-human IgG1 suggested: None anti-mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resour…

   SciScore for 10.1101/2020.06.30.177097: (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

   Antibodies
   Sentences	Resources
   Anti-RBD polyclonal antibody and monoclonal antibody (MAb) 1A10 were prepared by immunizing BALB/c mice with recombinant SARS-CoV-2 RBD fused with a C-terminal mouse IgGFc tag (Sino Biological Inc, Beijing, China) using previously described protocols (Qu et al., 2020).	Anti-RBD suggested: None
   After washing, the corresponding secondary antibodies, horseradish peroxidase (HRP)-conjugated anti-human IgG1 (Abcam, USA) or HRP-conjugated anti-mouse IgG (Sigma, USA), were added and incubated at 37°C for 1 h.	anti-human IgG1 suggested: None anti-mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The expression vectors were transiently transfected into HEK293F cells using polyethylenimine.	HEK293F suggested: RRID:CVCL_6642)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Anti-RBD polyclonal antibody and monoclonal antibody (MAb) 1A10 were prepared by immunizing BALB/c mice with recombinant SARS-CoV-2 RBD fused with a C-terminal mouse IgGFc tag (Sino Biological Inc, Beijing, China) using previously described protocols (Qu et al., 2020).	BALB/c suggested: None
   Software and Algorithms
   Sentences	Resources
   The movies were recorded on a K2 Summit direct electron detector (Gatan) operated in the super-resolution mode (yielding a pixel size of 1.02 Å after 2 times binning), under low-dose condition in an automatic manner using SerialEM (Mastronarde, 2005).	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   All images were aligned and summed using MotionCor2 software (Zheng et al., 2017).	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   For class 1, after further 2D classification, we refined the 24,502 cleaned up particles into a S-open map at 6.0 Å resolution using non-uniform refinement in CryoSparc.	CryoSparc suggested: (cryoSPARC, RRID:SCR_016501)
   The ACE2 associated with the up RBD was subtracted and refined in Relion to obtain a more 8.4 Å map with better connectivity.	Relion suggested: (RELION, RRID:SCR_016274)
   For the missing loop regions in S1 subunit, we either built the homology model based on SARS-CoV S structure (PDB: 6CRW) (Kirchdoerfer et al., 2018) through SWISS-MODEL webserver (Waterhouse et al., 2018), or built the loop manually according to the density in COOT (Emsley and Cowtan, 2004).	COOT suggested: (Coot, RRID:SCR_014222)
   For the FP region, we first built the homology model by Modeller tool within Chimera by using MERS-CoV S structure (PDB: 6NB3) as template (Pettersen et al.	Modeller suggested: (MODELLER, RRID:SCR_008395)
   We then refined the combined model against our 3.8 Å resolution SARS-CoV-2 S-ACE2 map using Rosetta and Phenix.	Phenix suggested: (Phenix, RRID:SCR_014224)
   Interaction surface analysis was conducted by PISA server (Krissinel and Henrick, 2007).	PISA suggested: (PISA, RRID:SCR_015749)

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   Results from OddPub: Thank you for sharing your data.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   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).

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 34 and 31. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   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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3. 

   Version published to 10.1101/2020.06.30.177097v1 on bioRxiv

   Jun 30, 2020