Virus structures articles within Nature Communications

Featured

  • Perspective
    | Open Access

    Recently, studies have identified different low-density lipoprotein receptors as functional entry receptors for alphaviruses. In this Perspective, the authors compare the known alphavirus-receptor structures and discuss why it might be challenging to generate a broad-spectrum entry inhibitor.

    • Ningning Wang
    • , Andres Merits
    •  & Shuo Su

  • Article
    | Open Access

    The viral polymerase complex is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses. Here, the authors link varying structures of polymerase complexes with their dual functions and propose a sliding model for them to advance along the RNA templates.

    • Tianhao Li
    • , Mingdong Liu
    •  & Qing-Tao Shen

  • Article
    | Open Access

    The structure and function of polymerase dimers of non-segmented, negative-strand RNA viruses are poorly understood. Here, this study presents the structural basis for dimerization of a paramyxovirus L–P polymerase and its role in genome replication.

    • Jin Xie
    • , Mohamed Ouizougun-Oubari
    •  & Shuai Chen

  • Article
    | Open Access

    The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Here, authors present the high-resolution cryo-EM structure of its intact tail machine, and identify multiple hydrolytic and binding modules.

    • Rong-Cheng Yu
    • , Feng Yang
    •  & Cong-Zhao Zhou

  • Article
    | Open Access

    Here, Li et al. provide the cryo-EM structures of Banna virus (BAV) in four configurations. VP10 functions as a unique cementing protein to stabilize the capsid shells and spikes in the full particles and during cell entry. Structural transition from BAV virions to cores is a stepwise process of dissociation of receptor binding protein VP9 and membrane penetration protein VP4.

    • Zhiqiang Li
    • , Han Xia
    •  & Sheng Cao

  • Article
    | Open Access

    Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is used as a bioinsecticide and a protein expression vector. Here, the authors report structures of cylindrical body of the AcMNPV nucleocapsid, as well as of both the nucleocapsid head and base.

    • Xudong Jia
    • , Yuanzhu Gao
    •  & Qinfen Zhang

  • Article
    | Open Access

    The severe fever with thrombocytopenia syndrome virus (SFTSV, officially named Dabie bandavirus) is a tick-borne human-infecting bunyavirus. Here, the authors report the cryo-EM structure of SFTSV virion, and discuss the mechanisms of viral assembly, membrane fusion and antibody neutralization.

    • Shouwen Du
    • , Ruchao Peng
    •  & Chang Li

  • Article
    | Open Access

    The authors explore the structural polymorphism of the Human Respiratory Syncytial Virus (HRSV) nucleocapsids, detect a non-canonical symmetry of the helical state resulting in variations in the genome accessibility, and reveal its molecular determinant.

    • Lorène Gonnin
    • , Ambroise Desfosses
    •  & Irina Gutsche

  • Article
    | Open Access

    Tailed bacteriophages account for the majority of all phages. Here, the authors employ cryo-EM and structure prediction techniques to investigate the atomic structure of the R4C phage capsid and the in- situ structure of its unique long rigid tail.

    • Yang Huang
    • , Hui Sun
    •  & Ningshao Xia

  • Article
    | Open Access

    In 2022, the zoonotic Langya virus caused cases of severe pneumonia in humans. Here, the authors determine the structure of the fusion glycoprotein of Langya virus and demonstrate antigenic but not structural divergence from bat-borne henipaviruses, yielding insights for future vaccine designs.

    • Ariel Isaacs
    • , Yu Shang Low
    •  & Daniel Watterson

  • Article
    | Open Access

    Safe delivery of genes is needed for gene therapy. Here the authors build “artificial viral vectors” (AVVs) by engineering the well-characterised structural components of bacteriophage T4: the large capacity, all-in-one, multiplex, programmable, and phage-based AVV nanomaterials have potential for gene therapy.

    • Jingen Zhu
    • , Himanshu Batra
    •  & Venigalla B. Rao

  • Article
    | Open Access

    Newcastle disease virus (NDV) belongs to Paramyxoviridae and encodes a large protein (L) and phosphoprotein (P) for viral RNA synthesis. Here the authors present cryo-EM structures of the L-P complex, and propose a model of how RNA initiation/elongation alternates during viral RNA synthesis.

    • Jingyuan Cong
    • , Xiaoying Feng
    •  & Zihe Rao

  • Article
    | Open Access

    HIV maturation inhibitors such as bevirimat (BVM) interfering with Gag processing are emerging as alternative anti-retroviral drug candidates. Here, the authors report structures of assemblies of HIV-1 Gag fragments spanning the CA C-terminal domain and SP1 region bound to BVM.

    • Sucharita Sarkar
    • , Kaneil K. Zadrozny
    •  & Tatyana Polenova

  • Article
    | Open Access

    Viruses can cause Colony Collapse Disorder, leading to large losses of honeybee hives globally. In this study, the authors solve capsid structures of honeybee-infecting Lake Sinai viruses and identify distinct features, which advances understanding of viral dynamics, assembly and infection mechanisms.

    • Nai-Chi Chen
    • , Chun-Hsiung Wang
    •  & Chun-Jung Chen

  • Article
    | Open Access

    Giant viruses are large DNA viruses with capsid diameters up to 500 nm. Given technical challenges only few high-resolution structures of viral capsids exist. Here, Shao et al. provide a nearatomic structure of giant virus PBCV-1 capsid and resolve the previously unknown asymmetric capsid components. The local capsid microenvironments created by these components provide insights into the mechanism of capsid assembly of giant viruses.

    • Qianqian Shao
    • , Irina V. Agarkova
    •  & Qianglin Fang

  • Article
    | Open Access

    VRC01-class bNAbs against the CD4 binding site of HIV-1 Env are targets of vaccine design. Here, the authors structurally characterized germline versions of the VRC01-class bNAb, BG24, bound to Env. They reveal mechanisms of germline binding, informing the design of VRC01-class targeting immunogens.

    • Kim-Marie A. Dam
    • , Christopher O. Barnes
    •  & Pamela J. Bjorkman

  • Article
    | Open Access

    Zhou and Si et al. used cryogenic electron microscopy and tomography to delineate the molecular interactions among genomic RNA, nucleocapsid protein, matrix protein and glycoprotein in vesicular stomatitis virus and suggest a model of assembly.

    • Kang Zhou
    • , Zhu Si
    •  & Z. Hong Zhou

  • Article
    | Open Access

    Enteroviruses are non-enveloped positive-sense RNA viruses that modulate cytoplasmic membranes for replication. To enlighten how enteroviruses assemble around nascent RNA genomes and get package into autophagosomes for release, Dahmane et al. perform cryo-electron tomography of poliovirus-infected cells. They find assembly intermediates that are only present on the cytosolic side of the replication compartment and provide evidence that host factor VPS34 is involved in progression of assembly intermediates.

    • Selma Dahmane
    • , Adeline Kerviel
    •  & Lars-Anders Carlson

  • Article
    | Open Access

    Immature poxviruses are characterized by nonicosahedral semiordered protein scaffolds critical for morphogenesis. Here, the authors use cryo-EM structures of Vaccinia virus D13 scaffold intermediates to explain their assembly mechanism.

    • Jaekyung Hyun
    • , Hideyuki Matsunami
    •  & Matthias Wolf

  • Article
    | Open Access

    Zhang and Cui et al. present in situ cryoEM structures of the trimeric spike of cytoplasmic polyhedrosis virus in both open and close conformations, and demonstrate that spike detachment from the capsid is triggered by the presence of SAM and ATP.

    • Yinong Zhang
    • , Yanxiang Cui
    •  & Z. Hong Zhou

  • Article
    | Open Access

    In this study, Peijun Zhang and colleagues use cryoFIB/SEM volume imaging and soft x-ray cryo-tomography with cryo-electron tomography (cryoET) of cellular periphery, lamellae, and subtomogram averaging to place critical structural events in the SARS-CoV-2 infection cycle in the context of whole-cell images.

    • Luiza Mendonça
    • , Andrew Howe
    •  & Peijun Zhang

  • Article
    | Open Access

    Mammalian reovirus (MRV) is a double-stranded RNA (dsRNA) virus that affects the gastrointestinal and respiratory tracts. Here, the authors present the 3.3 Å cryo-EM asymmetric reconstruction of transcribing MRV that reveals the organization of the dsRNA genome, RNA interaction with the polymerase complex, and how the polymerase interacts extensively with its co-factor, µ2, to form a transcription enzyme complex, which engages and regulates RNA transcription.

    • Muchen Pan
    • , Ana L. Alvarez-Cabrera
    •  & Z. Hong Zhou

  • Article
    | Open Access

    Secondary structures and long-range RNA interactions of the SARS-CoV-2 genome have been investigated by various sequencing methods. Here the authors use an RNA-RNA hybrid sequencing method to predict the secondary and tertiary structure of the SRAS-CoV-2 RNA genome in the virion.

    • Changchang Cao
    • , Zhaokui Cai
    •  & Yuanchao Xue

  • Article
    | Open Access

    SARS-CoV-2 viruses are known to hijack human proteins in order to facilitate their own virulence and replication. In this study, Liu and colleagues present structural analysis of how this phenomenon occurs between SARS-CoV-2 viral envelope protein and human PALS1. The findings provide insights in to viral-host recognition.

    • Jin Chai
    • , Yuanheng Cai
    •  & Qun Liu

  • Article
    | Open Access

    Understanding virus assembly could identify potential drug targets. Here the authors use a safe and efficient method to solve pathogenic flavivirus structures, revealing two lipid-like ligands within highly conserved pockets of the stem region of envelope protein that are important for virus maturation.

    • Joshua M. Hardy
    • , Natalee D. Newton
    •  & Daniel Watterson

  • Article
    | Open Access

    Inositol hexakisphosphate (IP6) is a known assembly cofactor for HIV-1. Here, the authors show the role of IP6 in the assembly of the Rous sarcoma virus (RSV). Reported cryo-ET structures of mature capsid-like particles (CLPs) suggest that IP6 modulates the formation of capsid polyhedrons of variable shape.

    • Martin Obr
    • , Clifton L. Ricana
    •  & Robert A. Dick

  • Article
    | Open Access

    The spike protein of coronaviruses (S-protein) is an envelope-anchored trimeric type I transmembrane glycoprotein that mediates receptor binding and the fusion of the viral and host cell membranes. Here the authors report the conformational states of HCoV-229E S trimer and observe the conformational changes in S1 subunit from closed state to activated state for receptor binding.

    • Xiyong Song
    • , Yuejun Shi
    •  & Guiqing Peng

  • Article
    | Open Access

    Here, the authors provide a 3.4 Å resolution structure of mature Zika virus (ZIKV) and identify two lipid moieties, coordinated by hydrophobic residues of the M and E transmembrane helices and between two helices of E protein, that play an essential role in the ZIKV assembly pathway.

    • Nadia M. DiNunno
    • , Daniel J. Goetschius
    •  & Joyce Jose

  • Article
    | Open Access

    Varicella-zoster virus (VZV) is the causative agent of chickenpox and herpes zoster (shingles). Cryo-EM structure of VZV capsid provides insights into the capsid assembly and reveals a pocket that could potentially be targeted by antiviral drugs.

    • Junqing Sun
    • , Congcong Liu
    •  & Peiyi Wang

  • Article
    | Open Access

    Human coronavirus-HKU1 contains two surface projections called spike and haemagglutinin-esterase (HE), with the latter acting as a receptor-destroying enzyme. Here, the authors use cryo-EM and mass spectrometry to characterise the small, heavily glycosylated HKU1 HE, revealing a vestigial lectin domain covered with a putative glycan shield; and they discuss these features in the context of host adaptation.

    • Daniel L. Hurdiss
    • , Ieva Drulyte
    •  & Raoul J. de Groot

  • Article
    | Open Access

    Flagellotropic phages spin down flagella to reach the bacterial surface and must withstand remarkable drag forces. Here authors show how two nested sets of chainmail stabilise the viral head and a beta-hairpin regulates the formation of the robust yet pliable tail, characteristic of siphoviruses.

    • Joshua M. Hardy
    • , Rhys A. Dunstan
    •  & Fasséli Coulibaly

  • Article
    | Open Access

    Rift Valley fever virus (RVFV) can cause severe diseases in humans, including encephalitis. Here the authors show that NSs, the major virulence factor of RVFV, is an amyloidogenic protein forming fibrils in infected mouse brains and causing increased mortality in mice.

    • Psylvia Léger
    • , Eliana Nachman
    •  & Pierre-Yves Lozach

  • Article
    | Open Access

    Gene transfer agents (GTAs) are phage-like particles that mediate lateral gene exchange. Here, the authors provide the structure of the GTA of Rhodobacter capsulatus (RcGTA), which resembles a tailed phage, and describe the conformational changes required for DNA ejection.

    • Pavol Bárdy
    • , Tibor Füzik
    •  & Pavel Plevka

  • Article
    | Open Access

    In icosahedral viruses, a symmetry-mismatched portal vertex is assembled by inserting a 12-fold-symmetric portal complex into a 5-fold-symmetric capsid environment. Here, the authors report a near-atomic-resolution in situ cryo-electron microscopy structure of this symmetrically mismatched viral vertex from bacteriophage T4.

    • Qianglin Fang
    • , Wei-Chun Tang
    •  & Venigalla B. Rao

  • Article
    | Open Access

    Here, using cryo-EM and smFRET, Henderson et al. show how tryptophan 571 in the HIV-1 Env acts as a conformational switch during receptor-mediated viral entry and design HIV-1 Env proteins that cannot undergo conformational changes. This has important implications for HIV-1 vaccine design.

    • Rory Henderson
    • , Maolin Lu
    •  & S. Munir Alam

  • Article
    | Open Access

    Respiratory syncytial virus (RSV) is a pathogenic non-segmented negative-sense RNA virus and active RSV polymerase is composed of a 250 kDa large (L) protein and tetrameric phosphoprotein (P). Here, the authors present the 3.67 Å cryo-EM structure of the RSV polymerase (L:P) complex.

    • Dongdong Cao
    • , Yunrong Gao
    •  & Bo Liang

Browse broader subjects

Browse Virus structures across other nature.com journals