Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure

Chen, L.; Wang, M.; Zhu, Dahuan; Sun, Zhenzhao; Ma, Jun; Wang, J.; Kong, Liangliang; Wang, Shizhuang; Liu, Z.; Wei, Lili; He, Yang-Hui; Zhang, X.

doi:10.1038/s41467-018-07704-x

Cited by 57 publications

(71 citation statements)

References 42 publications

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“…4f), suggesting that the binding pocket is conserved in flaviviruses. Notably, a functionally equivalent observation has recently been made in Sindbis alphavirus, where a lipid pocket factor was found buttressed in between the membrane associated helices of the glycoproteins 32 (Fig. 4g).…”

Section: Rearrangement Of Amphipathic Helices Leads To Formation Of Asupporting

confidence: 64%

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A high resolution view of an adolescent flavivirus

Renner

Dejnirattisai

Carrique

et al. 2020

Preprint

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Mosquito-transmitted flaviviruses, such as Dengue virus (DENV) or Zika virus (ZIKV), are responsible for significant economic damage and human misery. In infected cells, flaviviruses first assemble into an immature form within the endoplasmatic reticulum (ER), and then undergo further processing by furin protease in the trans-Golgi. Despite substantial efforts, previous cryogenic electron microscopy (cryo-EM) studies of immature flaviviruses were restricted to low to medium resolutions, limiting our understanding of maturation. To better grasp the process of maturation, we have carried out cryo-EM reconstructions of immature Spondweni virus (SPOV), an emerging human flavivirus belonging to the same serogroup as ZIKV (~75% amino acid identity). By combining localized reconstruction and focused refinement, we were able to improve the resolution to 3.8 Å, yielding unprecedented insight into the immature form. The structure elucidates how, at neutral pH, polar interactions conceal the furin recognition site within trimeric envelope (E) protein spikes. Furthermore, we identify how a strictly conserved pH sensor anchors the precursor membrane (prM) protein to immature E. We reconstructed mature forms of SPONV and DENV to 2.6Å and 3.1Å, respectively. Comparison with immature virus shows a conserved binding pocket for a lipid headgroup, which forms as a consequence of the rearrangement of amphipathic stem-helices of E. We propose a structural role for the pocket and suggest it stabilizes mature E. Taken together, our data suggest a compelling rationale for low-pH triggered conformational rearrangement in the Golgi, which occurs during flavivirus maturation. especially D. Clare, for assistance with data collection and advice on data processing. We also thank L. Mendonça, T. Frosio, and members of the P. Zhang group for scientific discussions.

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Section: Rearrangement Of Amphipathic Helices Leads To Formation Of Asupporting

confidence: 64%

“…4g). A histidine was also found packing against the pocket factor in this case, and has been suggested to be protonated at low pH during virus entry and to be involved in subsequent collapse of the lipid-binding pocket 32 .…”

Section: Rearrangement Of Amphipathic Helices Leads To Formation Of Amentioning

confidence: 74%

A high resolution view of an adolescent flavivirus

Renner

Dejnirattisai

Carrique

et al. 2020

Preprint

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“…2A, step 5). Recently the structure of the complete Sindbis virus (SINV) virion has been reconstructed this way from three separate subparticle reconstructions at 3.5 Å resolution (Chen et al, 2018).…”

Section: Single Particle Averaging and Localized Reconstructionmentioning

confidence: 99%

“…The same strategy has been applied to several members of the Togaviridae family. A cryo-EM structure of Sindbis virus (SINV; Togaviridae) at 3.5 Å resolution has allowed the identification of a "pocket factor," a 20-Å long molecule, possibly a phospholipid tail, projecting from the viral lipid bilayer into a membrane-proximal hydrophobic pocket of the GP shell (Chen et al, 2018). A chikungunya virus (CHIKV; Togaviridae) VLP structure has been determined at 5.3-Å resolution.…”

Section: Virions With Icosahedrally Symmetric Protein Shellsmentioning

confidence: 99%

Structures of enveloped virions determined by cryogenic electron microscopy and tomography

Stass

Kim

et al. 2019

Advances in Virus Research

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Enveloped viruses enclose their genomes inside a lipid bilayer which is decorated by membrane proteins that mediate virus entry. These viruses display a wide range of sizes, morphologies and symmetries. Spherical viruses are often isometric and their envelope proteins follow icosahedral symmetry. Filamentous and pleomorphic viruses lack such global symmetry but their surface proteins may display locally ordered assemblies. † These authors contributed equally.

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“…First, cryo-EM structures reveal that the E2 protein only contains a single TM domain in the context of the viral envelope. 23,24 Though it has been speculated that a second TM domain within E2 is somehow extruded from the membrane during processing, the marginal hydrophobicity of this segment also raises the possibility that it may fail to undergo translocon-mediated membrane integration in the first place. Second, the hydrophobic portion of the SINV 6K protein is only 35 residues in length, which is quite short for a segment containing two putative TM domains and a loop.…”

Section: Topological Properties Of the Alphavirus Structural Polyproteinmentioning

confidence: 99%

Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein

Harrington

Zimmer

Chamness

et al. 2019

Preprint

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Viruses maximize their genetic coding capacity through a variety of biochemical mechanisms including programmed ribosomal frameshifting (PRF), which facilitates the production of multiple proteins from a single transcript. PRF is typically stimulated by structural elements within the mRNA that generate mechanical tension between the transcript and ribosome. However, in this work we show that the forces generated by the cotranslational folding of the nascent polypeptide chain can also enhance PRF. Using an array of biochemical, cellular, and computational techniques, we first demonstrate that the Sindbis virus structural polyprotein forms two competing topological isomers during biosynthesis at the ribosome-translocon complex. We then show that the formation of one of these topological isomers is linked to PRF. Coarse-grained molecular dynamic simulations reveal that the translocon-mediated membrane integration of a transmembrane domain upstream from the ribosomal slip-site generates a force on the nascent polypeptide chain that scales with observed frameshifting. Together, our results demonstrate that cotranslational folding of this protein generates a tension that stimulates PRF. To our knowledge, this constitutes the first example in which the conformational state of the nascent chain has been linked to PRF. These findings raise the possibility that, in addition to RNA-mediated translational recoding, a variety of cotranslational folding and/ or binding events may also stimulate PRF.

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Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure

Cited by 57 publications

References 42 publications

A high resolution view of an adolescent flavivirus

A high resolution view of an adolescent flavivirus

Structures of enveloped virions determined by cryogenic electron microscopy and tomography

Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein

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