A structural model of L2 within the capsid is developed using cryo-EM single particle analysis of HPV16 pseudovirus capsids with and without the L2 protein combined with AlphaFold3 predictions and molecular dynamics simulations to develop a structural basis for understanding how L2 is organized in the capsid poised to initiate its action during virus entry.
Poxviruses are a family of large, complex double-stranded DNA viruses that includes human pathogens such as variola-the cause of smallpox-and monkeypox. Recent outbreaks of mpox underscore the need for a better understanding of poxvirus biology1,2. Poxvirus assembly is a conserved process that involves the formation of a biconcave core inside the membrane of the maturing virus3,4. Here we use cryo-electron tomography combined with subtomogram averaging and structure prediction to determine the structure and composition of the portal complex-a pore that spans the core wall-in vaccinia virus, the prototypical poxvirus. The hexameric complex consists of the E8, E6 and L3 proteins, which are conserved across poxviruses and essential for mRNA release during the establishment of infection5-7. E6, which is also required for virus assembly8-10, forms the central chamber of the portal and interacts with the surrounding core wall. A hexamer of E8 attaches to the exterior side of E6. L3, a target of TRIM5α-mediated restriction11, binds as a hexamer of dimers to the interior side. Furthermore, the viral helicase D5, which is required for genome release from cores12, associates with cytoplasmic cores during infection by docking onto the exterior E8 rim of the portal complex. We propose that the portal complex represents an attractive target for the development of anti-poxvirus therapeutics.
T. Calcraft, Miguel Hernández-González, Michael Way et al.· Nature· 0 citations
Nipah virus (NiV) is a BSL-4 zoonotic paramyxovirus with ∼75% human mortality. The matrix protein (M) of NiV and other paramyxoviruses binds the inner leaflet of the cellular plasma membrane, orchestrating virion assembly by bringing together transmembrane glycoproteins (F/G) and ribonucleoprotein complexes (N). However, the interactions of these full-length proteins within membrane complexes remain elusive. Using cryo-electron tomography and subtomogram averaging of virus like particles (VLPs), we interrogated the protein:protein interactions of the main NiV structural proteins M/N/F/G. The M lattice structure determined to 7Å revealed a novel M-dimer arrangement that yielded two distinct repeating holes. Notably, F-trimers were arranged above only one of the two holes, dependent on F’s cytoplasmic tail. G was enriched in regions of higher M-VLP curvature, while N dramatically increased M-VLP pleomorphism. This work provides novel insights into paramyxoviral protein complexes, structures, and morphology.
Viraj Upadhye, Jean F. Lee, Nihan Z. Ercanli et al.· bioRxiv· 0 citations
The small envelope protein of hepatitis B virus (S-HBs) is the principal component of the spherical and filamentous noninfectious subviral particles (SVPs) produced by infected hepatocytes, likely functioning as immune tolerizing agents critical to the establishment and maintenance of chronic infection. The structural features of S-HBs in the context of SVPs have been recently elucidated by several groups using high resolution cryo-EM techniques. In this review, we resolve the commonalities and differences between these reports. The basic unit of SVPs is an S-HBs dimer which is stabilized by hydrophobic interactions between adjacent protomer helices (TH2/TH2 and TH1/EH4, nomenclature by Wang et al., 2024), forming a helical transmembrane core. The adjacent protomer cytosolic and antigenic loops (CYL and AGL, respectively) contribute to dimer stability through salt bridges and intermolecular disulfide bonds; the CYL likely features a zinc finger motif coordinated by C48, H60, C65 and C69, which were shown to be essential. Oligomerization of dimers into trimeric and multiple tetrameric arrangements of dimers during SVP morphogenesis is aided by conformational plasticity within the helical core. Taking previous cell biological studies into account, it is envisioned that in the ER membrane topology and dimerization of S-HBs occur co-translationally, initiating an SVP budding process that completes in the downstream ERGIC and/or Golgi compartments. We report on the identification of two possible non-symmetrical small-molecule binding pockets at the dimer interface, and one in the CYL zing finger region. The druggability of these pockets, as well as unresolved issues in SVP biology, are discussed.
A. Cuconati, K. Fan, Gideon Tolufashe et al.· Antiviral Research· 0 citations
Influenza viruses belong to the Orthomyxoviridae family, they are categorized into four types: A, B, C, and D. Influenza B viruses co-circulate annually with influenza A strains during seasonal flu epidemics in humans, causing severe disease. The segmented RNA encapsidated by multiple copies of the nucleoprotein (NP) and attached to the heterotrimeric polymerase forms the central replicative unit called the viral ribonucleoprotein (vRNP). All influenza NP proteins share the same core domain folding, only NP of influenza B virus (B/NP) has an extended unfolded N-terminal tail of 70 amino-acids. This disordered N-terminal tail is required for nuclear localization of the protein, and may be involved in viral RNA transcription and replication regulation. In this study, we report that in absence of the extended N-terminal tail, the truncated NP maintains RNA binding ability and NP oligomeric state in vitro. We then reconstituted RNP-like particles by incubating truncated B/NP with synthetic RNA and we solved the cryo-EM structure at 4.1 Å resolution. Their morphology appears identical to native vRNPs extracted from viruses when observed by negative-stain electron microscopy. Overall, our results suggest that vRNPs from influenza virus type A, B and D share the same right-handed antiparallel helical conformation and that the B/NP N-terminal tail does not participate to the helical architecture stabilization once the vRNPs are assembled.
Marie Thirion, A. J. Stelfox, Florian Chenavier et al.· PLoS Pathogens· 0 citations
Human rhinoviruses (RV) cause severe socioeconomic problems and are also associated to, or exacerbate, severe respiratory diseases, but no anti-RV drugs are available so far. Understanding the functional role(s) of capsid-RNA interactions in the RV virion may contribute to antiviral drug development. Our previous studies showed that the genome inside the RV-B14 virion is organized as a capsid-bound RNA dodecahedral cage formed by 30 intrachain RNA duplexes; and that positively charged capsid residues close to each RNA duplex, including K4058 and K2052, are involved in viral infection by promoting virion assembly and controlling genome uncoating. In this study, cryogenic electron microscopy was used to investigate the structural basis that underlies the functional roles of those positively charged residues in the RV virion. The atomic structure and equilibrium conformation dynamics of mutant virions carrying either K4058A or K2052A substitutions were compared with those of the parental RV-B14 virion under identical conditions. The results showed that both K4058 and K2052 residues stabilize the RNA duplex structure, and modulate capsid conformation and equilibrium dynamics. Notably, the partially disorganized RNA elements in the K4058A mutant virion strongly resemble those previously found by other researchers in an alternative wild-type RV-B14 structure. Comparison of the two alternative wild-type virion structures and the mutant virion structures supports the existence of two conformational states of the RV virion in the absence of cell receptor: a basal state with well-structured RNA duplexes, and an activated, RNA release-prone state in which the RNA duplexes are partially disorganized.
Juan M. Martínez-Romero, Luis Valiente, J. Vilas et al.· Journal of Molecular Biology· 0 citations
Flaviviruses are globally distributed human pathogens. However, the mechanisms underlying flavivirus assembly and maturation remain poorly understood. Here, we show that many particles of tick-borne encephalitis virus (TBEV) are asymmetric and lack subsets of surface heterodimers. Immature particles of TBEV contain incomplete spikes, providing evidence that their coats assemble directly from heterodimers of premembrane (prM) and envelope (E) proteins. Exposure of TBEV particles to acidic pH in the Golgi complex promotes maturation. The spikes and herringbone regions in TBEV maturation intermediates are oriented randomly rather than conforming to a common icosahedral symmetry. Consequently, the mature herringbone lattice forms around a randomly oriented nucleation center, expanding by addition of membrane-envelope heterodimers as the spikes disassemble and prMs are cleaved. The observed incompleteness of the protein coats explains, as an alternative to particle breathing, how flaviviruses can be neutralized by antibodies that bind to regions of E proteins normally inaccessible in the spiky or herringbone structures.
Tibor Füzik, Maria Anastasina, Peter Pajtinka et al.· Science Advances· 0 citations
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MIT News · Artificial Intelligence· news.mit.eduAug 27, 2026
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.