Cryo-EM Captures the Step-by-Step Activation of the MERS-CoV Spike Protein

The Middle East respiratory syndrome coronavirus, or MERS-CoV, remains one of the most lethal human coronaviruses known to science, with case fatality rates far exceeding those of SARS-CoV-2. Yet the molecular events that transform its surface spike protein from a dormant, receptor-binding machine into an active fusion engine have long eluded structural biologists. A new study published in PLOS Pathogens by Yajie Wang, Xiyuan Pan, Yuxuan Jiang, Zhimin Liu, Yinong Qiu, Zhenguo Chen, and Lei Sun now fills in much of that missing sequence, using time-resolved cryo-electron microscopy to photograph the spike protein at successive stages of its activation journey. The work provides the most complete structural narrative to date of how receptor engagement on the viral surface is translated into the dramatic conformational upheaval that drives membrane fusion and viral entry.

Every coronavirus infection begins with the same fundamental transaction. The spike glycoprotein, a trimeric machine studded across the viral envelope, must recognize a receptor on the surface of a host cell, and that recognition event must somehow unlock the spring-loaded fusion machinery hidden in the spike’s stalk. For MERS-CoV, the relevant receptor is dipeptidyl peptidase 4, or DPP4, a membrane protein found on cells in the human respiratory tract and elsewhere. Although the structures of the receptor-binding domain bound to DPP4 have been known for years, those static snapshots could not explain how the binding of DPP4 is structurally coupled to the downstream act of membrane fusion. The new study was designed to close precisely that gap by watching the process unfold over time rather than capturing a single frozen moment.

The researchers turned to cryo-electron microscopy, a technique that flash-freezes protein complexes in vitreous ice and images thousands of individual particles to reconstruct high-resolution three-dimensional structures. Crucially, rather than incubating MERS-CoV spike with DPP4 for a single fixed period, the team determined structures of spike-DPP4 complexes at a series of defined incubation times. This time-course strategy allowed them to catch the spike in a succession of conformational states, spanning the prefusion conformation that exists before receptor contact, the receptor-bound intermediates that follow, and ultimately the postfusion conformation in which the fusion machinery has fired. The resulting gallery of structures amounts to a molecular filmstrip of spike activation, revealing intermediate states that a single time point would almost certainly have missed.

The first act of the story concerns the receptor-binding domain, or RBD, the upward-facing module at the top of each spike protomer that reaches out to grasp DPP4. Coronaviruses spikes exist in equilibrium between a closed state, in which all RBDs are tucked down against the trimer, and open states, in which one or more RBDs hinge upward to expose the receptor-binding surface. The time-course structures show that RBD opening is not a binary switch but a progressive process, and that as the RBDs open, the interactions holding the S1 subunit, which contains the RBDs, to the S2 subunit, which contains the fusion machinery, are progressively weakened. Receptor binding thus acts as a wedge, gradually prying apart the S1-S2 interface that normally keeps the spike locked in its metastable prefusion state.

The second act is subtler and, in some respects, more surprising. The structures suggest that DPP4 binding does more than simply hold the RBD open. The receptor appears to induce conformational drift and a loosening of the S2 fusion core, the tightly packed central element that stores the energy required for membrane merger. In the prefusion state, the S2 core is compressed like a coiled spring, and premature triggering would render the spike useless. The new data indicate that receptor engagement may destabilize this core from a distance, loosening the packing interactions that restrain the spring. In this view, DPP4 does not merely unlock the door to the cell; it also begins to shake the very mechanism that will eventually force the viral and cellular membranes together.

These cumulative structural changes, the authors propose, destabilize the spike trimer as a whole, promoting the dissociation of the S1 subunit from the viral surface. S1 shedding is a critical checkpoint in coronavirus entry: once S1 departs, the S2 subunit is freed to extend, insert its fusion peptide into the host membrane, and collapse into its postfusion hairpin. The time-course structures capture the priming of this fusion machinery, showing how the gradual erosion of intersubunit contacts converts receptor binding, an event on the outside of the virus, into the unleashing of a membrane-fusion engine anchored in the viral envelope. The study thus supplies a structural pathway connecting the two halves of the entry process that had previously been studied largely in isolation.

One of the most consequential findings emerges from a comparison with SARS-CoV-2, the virus responsible for the COVID-19 pandemic. When the MERS-CoV spike is set against its better-studied cousin, the MERS-CoV spike exhibits markedly greater conformational plasticity, sampling a wider range of states and transitioning between them more readily. This flexibility, the authors note, is consistent with a lower threshold for receptor-induced fusion. In practical terms, the MERS-CoV spike appears to sit closer to its triggering point, requiring less energetic provocation from receptor binding to commit to fusion. Such differences in activation energetics may help explain why coronaviruses with similar overall architectures can behave so differently in host cells, and they underscore that spike dynamics, not just spike sequence, are a critical determinant of viral entry behavior.

The postfusion S2 structure yielded an additional insight into the final assembly step of fusion. After the fusion peptide inserts into the host membrane, the heptad repeat regions of S2 fold back on themselves to form a six-helix bundle, the structure whose formation provides the energy that pulls the two membranes together. The new postfusion structure suggests that the linker region upstream of heptad repeat 2, the HR2 upstream linker, may function as a conformational switch during six-helix bundle assembly. Rather than serving as a passive tether, this linker appears positioned to regulate how the HR2 segments fold back onto the central coiled coil, potentially controlling the timing and efficiency of the final refolding step. If confirmed, this would add a previously underappreciated regulatory element to the coronavirus fusion mechanism.

Beyond its immediate findings on MERS-CoV, the study carries broader implications for structural virology and antiviral development. Time-course cryo-EM, as demonstrated here, offers a way to traverse the conformational landscape of a metastable viral machine without the need for triggering cues that might destroy the very intermediates of interest. The intermediate states captured along the MERS-CoV activation pathway are, by their nature, transient and difficult to study, yet they represent moments when the spike is neither fully closed nor fully fired, and therefore potentially vulnerable. Antibodies or small molecules that bind to such intermediates, or that stabilize the prefusion state against the loosening described in this study, could in principle block entry before the fusion machinery commits.

The authors frame their work as outlining a structural pathway for receptor-induced activation of the MERS-CoV spike and as providing a framework for antiviral strategies that target dynamic fusion intermediates. Given the persistent threat posed by MERS-CoV, which continues to cause sporadic severe outbreaks in the Middle East and remains on the World Health Organization’s list of priority pathogens, and given the broader need to understand how betacoronavirus spikes respond to their receptors, the structures reported here offer both a detailed mechanistic account and a practical template. By showing exactly how receptor binding weakens S1-S2 interactions, destabilizes the S2 fusion core, promotes S1 shedding, and primes the six-helix bundle transition, the study converts a decade of fragmentary structural observations into a coherent, time-ordered narrative of coronavirus entry, one that researchers targeting the fusion process across the coronavirus family will be able to build upon.

Subject of Research: Structural mechanism of DPP4 receptor-induced activation of the MERS-CoV spike glycoprotein revealed by time-course cryo-electron microscopy

Article Title: Receptor-induced activation of MERS-CoV spike revealed by time-course cryo-EM

Article References: Wang, Y., Pan, X., Jiang, Y., Liu, Z., Qiu, Y., Chen, Z., & Sun, L. (2026). Receptor-induced activation of MERS-CoV spike revealed by time-course cryo-EM. PLOS Pathogens, 22(10), e1014545. https://doi.org/10.1371/journal.ppat.1014545

Image Credits: AI Generated

DOI: 10.1371/journal.ppat.1014545

Keywords: MERS-CoV, spike protein, cryo-EM, DPP4 receptor, membrane fusion, S1-S2 processing, RBD opening, six-helix bundle, conformational plasticity, viral entry, PLOS Pathogens, structural virology