Electron microscopy articles within Nature Communications

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  • Article
    | Open Access

    Virus assembly is technically challenging to study. Here the authors use cryo-electron tomography of measles virus-infected human cells to determine native-state virus structure and they locate well-ordered M lattices that organize viral glycoproteins, RNP, and drive assembly.

    • Zunlong Ke
    • , Joshua D. Strauss
    •  & Elizabeth R. Wright

  • Article
    | Open Access

    Some prokaryotes use alternative respiratory chain complexes, such as the alternative complex III (ACIII), to generate energy. Here authors provide the cryoEM structure of ACIII from Rhodothermus marinus which shows the arrangement of cofactors and provides insights into the mechanism for energy transduction.

    • Joana S. Sousa
    • , Filipa Calisto
    •  & Manuela M. Pereira

  • Article
    | Open Access

    Kinesin-13s are microtubule depolymerases that lack motile activity. Here the authors present the cryo-EM structures of kinesin-13 microtubule complexes in different nucleotide bound states, which reveal how ATP hydrolysis is linked to conformational changes and propose a model for kinesin induced depolymerisation.

    • Matthieu P.M.H. Benoit
    • , Ana B. Asenjo
    •  & Hernando Sosa

  • Article
    | Open Access

    Main-chain tracing remains a time-consuming task for medium resolution cryo-EM maps. Here the authors describe MAINMAST, a computational approach for building main-chain structure models of proteins from EM maps of 4-5 Å resolution that builds main-chain models of the protein by tracing local dense points in the density distribution.

    • Genki Terashi
    •  & Daisuke Kihara

  • Article
    | Open Access

    Conventional reconstruction methods used in cryo-EM single particle analysis do not take the depth of field effect into account. Here the authors present a block-based reconstruction method to deal with the depth of field effect and show that this approach can improve the resolution of cryo-EM virus structures.

    • Dongjie Zhu
    • , Xiangxi Wang
    •  & Xinzheng Zhang

  • Article
    | Open Access

    The R2TP/PFDL co-chaperone facilitates assembly of RNA polymerase II and PI3-kinase-like kinases such as mTOR by a so far unknown mechanism. Here authors provide the cryo-EM structure of human R2TP, which shows how RPAP3 serves as a flexible platform to recruit HSP90 to diverse client proteins.

    • Fabrizio Martino
    • , Mohinder Pal
    •  & Oscar Llorca

  • Article
    | Open Access

    The 26S proteasome consists of a core particle that is capped at each side by a regulatory particle. Here the authors present cryo-EM structures of the activated human 26S proteasome holoenzyme in three alternative open-gate states, which provides mechanistic insights into gate opening and dynamic remodeling of the substrate–translocation pathway.

    • Yanan Zhu
    • , Wei Li Wang
    •  & Youdong Mao

  • Article
    | Open Access

    Nucleosomes are dynamic and can move along DNA in an uncatalyzed manner but little is known about the mechanisms of histone octamer translocation. Here the authors present cryo-EM structures of nucleosomes in differently organized histone octamer and DNA states and show how histone octamers translocate DNA.

    • Silvija Bilokapic
    • , Mike Strauss
    •  & Mario Halic

  • Article
    | Open Access

    Polycystic kidney disease 2-like 1 protein (PKD2L1) is a voltage-dependent calcium-dependent nonselective ion channel involved in sour taste perception and regulation of pH-dependent action potential of spinal cord neurons. Here the authors present the 3.4 Å cryo-EM structure of PKD2L1 in the open state and propose a model for the gating mechanism.

    • Qiang Su
    • , Feizhuo Hu
    •  & Tingliang Wang

  • Article
    | Open Access

    The NuA4 histone acetyltransferase complex is important for gene regulation, DNA repair processes and cell cycle progression. Here the authors give molecular insights into the NuA4 complex by presenting the cryo-EM structures of the NuA4 TEEAA (Tra1, Eaf1, Eaf5, actin, and Arp4) and TEEAA-piccolo NuA4 assemblies.

    • Xuejuan Wang
    • , Salar Ahmad
    •  & Gang Cai

  • Article
    | Open Access

    Teneurins are cell-cell adhesion receptors that evolved through horizontal gene transfer in which a bacterial YD-repeat protein fused to a eukaryotic receptor. Here the authors present crystallographic and cryo-EM structures of two Teneurins, revealing an ancient YD-repeat protein super-fold.

    • Verity A. Jackson
    • , Dimphna H. Meijer
    •  & Elena Seiradake

  • Article
    | Open Access

    Na+-coupled acid-base membrane transport proteins regulate blood pressure, ion homeostasis and acid-base chemistry. Here the authors present the 3.9 Å resolution cryoEM structure of the sodium-bicarbonate cotransporter NBCe1 and characterize its ion coordination site and ion accessibility pathway with mutagenesis experiments.

    • Kevin W. Huynh
    • , Jiansen Jiang
    •  & Ira Kurtz

  • Article
    | Open Access

    Amyloid fibril structures can display polymorphism. Here the authors reveal the cryo-EM structures of several different fibril morphologies of a peptide derived from an amyloidogenic immunoglobulin light chain and present a mathematical analysis of physical factors that influence fibril polymorphism.

    • William Close
    • , Matthias Neumann
    •  & Marcus Fändrich

  • Article
    | Open Access

    Scaffolded DNA origami by folding single-stranded DNA into three-dimensional nanostructures holds promise for building functional nanomachines, yet their dynamic structures remain largely unknown. Here, Lei et al. address this issue using individual-particle electron tomography at 6–14 nm resolution.

    • Dongsheng Lei
    • , Alexander E. Marras
    •  & Gang Ren

  • Article
    | Open Access

    Serotonin receptor (5-HT3AR), a pentameric ligand-gated ion channel, regulates numerous gastrointestinal functions. Here the authors provide a cryo-electron microscopic structure from the full-length 5-HT3AR in the apo-state which corresponds to a resting conformation of the channel.

    • Sandip Basak
    • , Yvonne Gicheru
    •  & Sudha Chakrapani

  • Article
    | Open Access

    The tick-borne encephalitis virus (TBEV) causes thousands of cases of meningitis and encephalitis annually. Here, the authors describe a cryo-EM structure of the TBEV virion bound by Fab fragments of the neutralizing antibody 19/1786, revealing a mechanism whereby this antibody prevents virus membrane fusion.

    • Tibor Füzik
    • , Petra Formanová
    •  & Pavel Plevka

  • Article
    | Open Access

    Viral fusion proteins undergo extensive conformational changes during entry but intermediate conformations often remain unknown. Here, the authors show how Gn of Rift Valley fever virus fusion protein shields hydrophobic fusion loops of Gc and how these loops embed in the target membrane at acidic conditions.

    • Steinar Halldorsson
    • , Sai Li
    •  & Juha T. Huiskonen

  • Article
    | Open Access

    Pex1 and Pex6 form a heterohexameric Type-2 AAA-ATPase motor whose function in peroxisomal matrix-protein import is still debated. Here, the authors combine structural, biochemical, and cell-biological approaches to show that Pex1/Pex6 is a protein unfoldase, which supports a role in mechanical unfolding of peroxin proteins.

    • Brooke M. Gardner
    • , Dominic T. Castanzo
    •  & Andreas Martin

  • Article
    | Open Access

    H+-ATPases employ a rotary catalytic mechanism to couple ATP synthesis/hydrolysis with proton translocation through the membrane. Here, the authors use high-resolution cryoEM to characterize three rotational states of a bacterial H+-ATPase, providing a more detailed model of its catalytic mechanism.

    • Atsuko Nakanishi
    • , Jun-ichi Kishikawa
    •  & Ken Yokoyama

  • Article
    | Open Access

    The prenyl-binding protein PrBP/δ is a solubilization factor involved in trafficking of prenylated proteins. Here the authors present the ligand-free apo-PrBP/δ structure and propose a "solubilization by depletion" mechanism, where PrBP/δ sequesters only soluble rod photoreceptor phosphodiesterase (PDE6), leading to a dissociation of membrane-bound PDE6.

    • Bilal M. Qureshi
    • , Andrea Schmidt
    •  & Patrick Scheerer

  • Article
    | Open Access

    Origins of replication are licensed by loading of MCM onto DNA, and origin firing depends on interaction with Cdc45 and GINS to form two CMG holo-helicases. Here, authors determine the cryo-EM structures of DNA-bound MCM and visualise a phospho-dependent MCM element important for Cdc45 recruitment.

    • Ferdos Abid Ali
    • , Max E. Douglas
    •  & Alessandro Costa

  • Article
    | Open Access

    MICAL Redox enzymes post-translationally modify F-actin to promote its cellular destabilization. Here, the authors present a 3.9Å cryoEM structure of Mical-oxidized F-actin, showing its nucleotide-state dependent dynamic instability and susceptibility to cofilin-induced severing in the presence of inorganic phosphate.

    • Elena E. Grintsevich
    • , Peng Ge
    •  & Emil Reisler

  • Article
    | Open Access

    Microtubules are vital and highly conserved components of the cytoskeleton. Here the authors carry out a structural analysis of fission yeast microtubules in the presence and absence of the microtubule end-binding protein Mal3 that demonstrates structural plasticity amongst microtubule polymers.

    • Ottilie von Loeffelholz
    • , Neil A. Venables
    •  & Carolyn A. Moores

  • Article
    | Open Access

    The BRICHOS domain is a chaperone that can act against amyloid-β peptide fibril formation and non-fibrillar protein aggregation. Here the authors use a multidisciplinary approach and show that the Bri2 BRICHOS domain has qualitatively different chaperone activities depending on its quaternary structure.

    • Gefei Chen
    • , Axel Abelein
    •  & Jan Johansson

  • Article
    | Open Access

    Many Gram-negative bacteria secrete exopolysaccharides via functionally homologous synthase-dependent systems. Here the authors use electron microscopy to reveal that biofilm-promoting cellulose in E. coli is secreted by a conserved multi-component secretion system with a megadalton-sized asymmetric architecture.

    • Petya Violinova Krasteva
    • , Joaquin Bernal-Bayard
    •  & Jean-Marc Ghigo

  • Article
    | Open Access

    Host cell recognition is mediated by the phage tail tip proteins, which then triggers viral genome delivery via the phage tail. Here, the authors combine crystallography and cryoEM to structurally characterise the bacteriophage T5 tail tube structure before and after interaction with its host receptor.

    • Charles-Adrien Arnaud
    • , Grégory Effantin
    •  & Cécile Breyton

  • Article
    | Open Access

    Target of rapamycin (TOR) kinase operates within two distinct multiprotein complexes named TORC1 and TORC2. Here the authors report a cryo-EM structure of TORC2, establish its subunit organization, providing a rationale for TORC2’s rapamycin insensitivity and the mutually exclusive inclusion of Avo3/Rictor or Raptor within their respective TOR complex.

    • Manikandan Karuppasamy
    • , Beata Kusmider
    •  & Christiane Schaffitzel

  • Article
    | Open Access

    Immunoproteasome selective inhibitors might lead to less toxic drugs for treatment of multiple myeloma and graft rejection. Here, the authors develop immunoproteasome specific asparagine-ethylenediamine (AsnEDA)-based inhibitory compounds, demonstrate their efficacy and present the AsnEDA bound immunoproteasome cryo-EM structure.

    • Ruda de Luna Almeida Santos
    • , Lin Bai
    •  & Gang Lin

  • Article
    | Open Access

    Leishmaniasis is a parasitic disease transmitted by the bite of infected sand flies. Here the authors describe an atomic resolution cryo-EM structure of the Leishmania ribosome in complex with the recently approved drug paromomycin (PAR) and highlight conserved elements in the drug binding pocket that mediate PAR deleterious effects on the parasite.

    • Moran Shalev-Benami
    • , Yan Zhang
    •  & Georgios Skiniotis

  • Article
    | Open Access

    The transcription co-activator complex SAGA is recruited to promoters by transcriptional activators and promotes the formation of the pre-initiation complex. Here, the authors present the cryo-EM structure of the SAGA complex and resolve the major target of activator binding, the 430 kDa Tra1 protein.

    • Grigory Sharov
    • , Karine Voltz
    •  & Patrick Schultz

  • Article
    | Open Access

    tRNA-dependent cysteine biosynthesis is catalyzed by the transsulfursome protein complex. Here, the authors use a multidisciplinary approach to structurally characterize the archaeal transsulfursome and propose a model for tRNA channeling in the complex.

    • Meirong Chen
    • , Koji Kato
    •  & Min Yao

  • Article
    | Open Access

    The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.

    • Denis Ptchelkine
    • , Ashley Gillum
    •  & Juha T. Huiskonen

  • Article
    | Open Access

    CRISPR-Cas9 is widely used for genome engineering but structural data for the DNA cleavage step are still incomplete. Here, the authors present the cryo-EM structure of a ternary Cas9-sgRNA-target DNA complex, perform MD simulations and discuss implications for the Cas9 DNA cleavage mechanism.

    • Cong Huai
    • , Gan Li
    •  & Qiang Huang

  • Article
    | Open Access

    The disease causing L253P mutation in the actin-binding domain (ABD) of β-III-spectrin drastically increases actin-binding affinity. Here, the authors present the cryo-EM structure of F-actin complexed with the ABD mutant and double electron–electron resonance measurements show how the mutation affects the ABD conformational state.

    • Adam W. Avery
    • , Michael E. Fealey
    •  & Edward H. Egelman

  • Article
    | Open Access

    The bacterial zinc transporter ZntB is important for maintaining zinc homeostasis and is mechanistically not well understood. Here, the authors present the cryo-EM structure of ZntB at 4.2 Å resolution, perform transport assays and propose a model for its Zn2+ transport mechanism.

    • Cornelius Gati
    • , Artem Stetsenko
    •  & Albert Guskov

  • Article
    | Open Access

    Bacterial flagellar filaments are composed almost entirely of a single protein—flagellin—which can switch between different supercoiled states in a highly cooperative manner. Here the authors present near-atomic resolution cryo-EM structures of nine flagellar filaments, and begin to shed light on the molecular basis of filament switching.

    • Fengbin Wang
    • , Andrew M. Burrage
    •  & Edward H. Egelman

  • Article
    | Open Access

    The B-cell-specific co-receptor CD22 is a therapeutic target for depleting dysregulated B cells. Here the authors structurally characterize the ectodomain of CD22 and present its crystal structure with the bound therapeutic antibody epratuzumab, which gives insights into the mechanism of inhibition of B-cell activation.

    • June Ereño-Orbea
    • , Taylor Sicard
    •  & Jean-Philippe Julien

  • Article
    | Open Access

    When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.

    • Linda E. Franken
    • , Gert T. Oostergetel
    •  & Albert Guskov

  • Article
    | Open Access

    Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.

    • Donna Matzov
    • , Shintaro Aibara
    •  & Ada E. Yonath

  • Article
    | Open Access

    Coxsackievirus A6 (CVA6) causes hand, foot and mouth disease in children. Here the authors present the CVA6 procapsid and A-particle cryo-EM structures and identify an immune-dominant neutralizing epitope, which can be exploited for vaccine development.

    • Longfa Xu
    • , Qingbing Zheng
    •  & Ningshao Xia

  • Article
    | Open Access

    The loading and activation of the Mcm2-7 replicative helicase couples cell cycle progression to DNA replication. Here the authors use X-ray crystallography and single-particle electron microscopy to demonstrate how Ctd1 functions to promote MCM loading onto DNA.

    • Jordi Frigola
    • , Jun He
    •  & John F. X. Diffley

  • Article
    | Open Access

    Phytoplankton and plant plastids have distinct evolutionary origins and membrane organization. Here Floriet al. show that diatom photosynthetic complexes spatially segregate into interconnected subdomains within loose thylakoid stacks enabling fast diffusion of electron carriers and efficient photosynthesis

    • Serena Flori
    • , Pierre-Henri Jouneau
    •  & Giovanni Finazzi

  • Article
    | Open Access

    Ca2+/calmodulin-dependent protein kinase II (CaMKII) forms a 12 subunit holoenzyme central to synaptic plasticity. Here the authors report a 3D structure of the CaMKII holoenzyme in an activation-competent state obtained by single particle EM, and suggest a role for the intrinsically disordered linker domain in facilitating cooperative activation.

    • Janette B. Myers
    • , Vincent Zaegel
    •  & Steve L. Reichow

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