Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations

  1. Tzu-Jing Yang
  2. Pei-Yu Yu
  3. Yuan-Chih Chang
  4. Kang-Hao Liang
  5. Hsian-Cheng Tso
  6. Meng-Ru Ho
  7. Wan-Yu Chen
  8. Hsiu-Ting Lin
  9. Han-Chung Wu
  10. Shang-Te Danny Hsu

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Abstract

The UK variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), known as B.1.1.7, harbors several point mutations and deletions on the spike (s) protein, which potentially alter its structural epitopes to evade host immunity while enhancing host receptor binding. Here we report the cryo-EM structures of the S protein of B.1.1.7 in its apo form and in the receptor ACE2-bound form. One or two of the three receptor binding domains (RBDs) were in the open conformation but no fully closed form was observed. In the ACE-bound form, all three RBDs were engaged in receptor binding. The B.1.1.7-specific A570D mutation introduced a salt bridge switch that could modulate the opening and closing of the RBD. Furthermore, the N501Y mutation in the RBD introduced a favorable π-π interaction manifested in enhanced ACE2 binding affinity. The N501Y mutation abolished the neutralization activity of one of the three potent neutralizing antibodies (nAbs). Cryo-EM showed that the cocktail of other two nAbs simultaneously bound to all three RBDs. Furthermore, the nAb cocktail synergistically neutralized different SARS-CoV-2 pseudovirus strains, including the B.1.1.7.

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    SciScore for 10.1101/2021.05.11.443686: (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

    Experimental Models: Cell Lines
    SentencesResources
    Recombinant sfGFP-ACE2 was transiently expressed in Expi293 cell and secreted into the culture medium.
    Expi293
    suggested: RRID:CVCL_D615)
    Pseudovirus neutralization assay: The pseudovirus neutralization assays were performed using 293T cells overexpressing ACE2 and pseudoviruses expressing full-length S protein provided by RNAi Core of Academic Sinica
    293T
    suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
    Recombinant DNA
    SentencesResources
    The DNA sequence corresponding the residues 1-1208 of S-UK was subcloned into the mammalian expression vector pcDNA3.4-TOPO (Invitrogen), which contains a foldon trimerization domain based on phage T4 fibritin followed by a c-myc epitope and a hexa-repeat histidine tag as described previously28.
    pcDNA3.4-TOPO
    suggested: None
    Expression and purification of sfGFP-ACE2: The sfGFP-ACE2 construct was obtained from Addgene (Plasmid #145171), which was deposited by Erik Proco (University of Illinois,
    sfGFP-ACE2
    suggested: None
    Software and Algorithms
    SentencesResources
    After motion correction, all corrected micrographs then were transferred to cryoSPARC v2.1432.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    The cumulated epitope counts were mapped onto the crystal structure of RBD in complex with ACE2 (PDB accession code 6M0J) and rendered by using Pymol (Schrodinger Inc. U. S. A.).
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    IC50 was determined by a four-parameter logistic regression using GraphPad Prism (GraphPad Software Inc.).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We did not find any issues relating to colormaps.

    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.

    Results from scite Reference Check: We found no unreliable references.

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  2. Version published to 10.1101/2021.05.11.443686v1 on bioRxiv