Electron microscopy articles within Nature Communications

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  • Article
    | Open Access

    The Paf1 complex (Paf1C) is an elongation factor assembly that forms the interface between transcribing Pol II and chromatin factors. Here the authors describe the architecture of Paf1C and its interface with Pol II, and show that Paf1C is globally required for normal mRNA transcription in yeast.

    • Youwei Xu
    • , Carrie Bernecky
    •  & Patrick Cramer

  • Article
    | Open Access

    The proteasome regulates several important cellular processes and has been identified as a target for therapeutic interventions. Here the authors map the conformational and energy landscape of the 26S proteasome upon Oprozomib binding and uncover long-range allosteric effects that control the dynamic behaviour of the proteasome.

    • David Haselbach
    • , Jil Schrader
    •  & Holger Stark

  • Article
    | Open Access

    Membrane proteins are inserted co-transnationally through the association between ribosome, the signal recognition particle and its receptor, and the membrane-bound translocon. Here the authors present a cryo-EM reconstruction of this quaternary complex in the activated state and propose a model for signal sequence transfer to the translocon.

    • Ahmad Jomaa
    • , Yu-Hsien Hwang Fu
    •  & Nenad Ban

  • Article
    | Open Access

    A connection between centrosomes and chromosomes is a key feature of mitotic spindles. Here the authors generate 3D reconstructions of whole mitotic spindles in earlyC. elegansembryos and show that chromosomes are anchored by the entire spindle network and that connections through kinetochore microtubules are few and likely very transient.

    • Stefanie Redemann
    • , Johannes Baumgart
    •  & Thomas Müller-Reichert

  • Article
    | Open Access

    Cilia are hair-like appendages involved in cell motility and sensory reception. Here, the authors report a high resolution cryo-EM structure of the microtubule doublet from motile cilia and identify microtubule inner proteins (MIPs) bound to the inner surface of the doublet that appear to stabilize its structure.

    • Muneyoshi Ichikawa
    • , Dinan Liu
    •  & Khanh Huy Bui

  • Article
    | Open Access

    Host tropism and cell entry of pathogenic coronaviruses are mediated by their envelope spike (S) proteins. Here the authors present structural analyses of trimeric MERS-CoV and SARS-CoV S proteins in pre-fusion conformation, and reveal two states of the receptor binding domain that suggest new avenues for the generation of neutralizing antibodies.

    • Yuan Yuan
    • , Duanfang Cao
    •  & George F. Gao

  • Article
    | Open Access

    The centriole is an organelle composed of rings of SAS-6 proteins that form a cartwheel structure. Here the authors develop a cell-free system to examine core cartwheel assembly ofC. reinhardtiiproteins and discover that CrSAS-6 has autonomous properties that facilitates self-organized stacking of pairs of rings.

    • P. Guichard
    • , V. Hamel
    •  & P. Gönczy

  • Article
    | Open Access

    The human monoclonal antibody ZIKV-117 has demonstrated therapeutic potential against Zika while showing no cross-reactivity to other flaviviruses. Here the authors present a cryo-EM structure of the ZIKV strain H/PF/2013 in complex with the ZIKV-117 Fab, shedding light on its neutralization mechanism.

    • S. Saif Hasan
    • , Andrew Miller
    •  & Michael G. Rossmann

  • Article
    | Open Access

    Double-shelled bacteriophage φ6 is a well-studied model system used to understand assembly of dsRNA viruses. Here the authors report a near-atomic resolution cryo-EM structure of φ6 and propose a model for the structural transitions occurring in the outer shell during genome packaging.

    • Zhaoyang Sun
    • , Kamel El Omari
    •  & Juha T. Huiskonen

  • Article
    | Open Access

    Self-assembling proteins that form capsid-like structures act as molecular containers for diverse cargoes. Here, the authors solve the cryo-EM structures of lumazine synthase shells, and show that supercharged mutants form expanded assemblies, indicating that electrostatics can be exploited to engineer cage architecture.

    • Eita Sasaki
    • , Daniel Böhringer
    •  & Donald Hilvert

  • Article
    | Open Access

    The translocon-associated protein complex (TRAP) is a crucial component of the endoplasmic reticulum protein translocon. Here the authors study native translocon structures from human disease patients and algae cells to determine the molecular organization of the TRAP complex.

    • Stefan Pfeffer
    • , Johanna Dudek
    •  & Friedrich Förster

  • Article
    | Open Access

    The bacterial flagellum is a motile organelle that enables bacterial movement. Here the authors explain how the structurally similar flagellum components FlgG and FlgE can give rise to distinct macrostructures—the rod and hook—through subtle differences in domain orientation attributable to a short N-terminal insertion in FlgG.

    • Takashi Fujii
    • , Takayuki Kato
    •  & Keiichi Namba

  • Article
    | Open Access

    mRNA surveillance is essential to maintain homeostasis in eukaryotes and is activated by mRNAs lacking a stop codon. Here the authors describe a high resolution cryo-EM structure of a nonstop complex that shows how arrested ribosome recognition is achieved during Dom34-mediated mRNA surveillance.

    • Tarek Hilal
    • , Hiroshi Yamamoto
    •  & Christian M.T. Spahn

  • Article
    | Open Access

    Two competing models—disassembly/reassembly and displacive—have been proposed for how immature spherical HIV virions transform into mature particles with conical cores. Here the authors provide evidence that both disassembly/reassembly and displacive processes occur sequentially during the maturation process.

    • Jiying Ning
    • , Gonca Erdemci-Tandogan
    •  & Peijun Zhang

  • Article
    | Open Access

    Gap junctions have critical roles in maintaining homeostasis in multicellular organisms. Here the authors present cryo-EM structures of the C. elegansinnexin-6 gap junction channel, revealing high structural similarity to human connexin 26 despite a different oligomeric number and lack of sequence similarity.

    • Atsunori Oshima
    • , Kazutoshi Tani
    •  & Yoshinori Fujiyoshi

  • Article
    | Open Access

    There is a pressing need for therapeutic agents against Zika virus (ZIKV). Here the authors present cryoEM structures of a neutralizing antibody (C10) complexed with ZIKV that show C10 preventing structural changes required for virus entry into the cell, suggesting it might be effective in treating Zika infections.

    • Shuijun Zhang
    • , Victor A. Kostyuchenko
    •  & Shee-Mei Lok

  • Article
    | Open Access

    Ribosome recycling orchestrated by ABCE1 connects translation termination and mRNA surveillance mechanisms with re-initiation. Using a cross-linking and mass spectrometry approach, Kiosze-Becker et al. provide new information on the large conformational rearrangements that occur during ribosome recycling.

    • Kristin Kiosze-Becker
    • , Alessandro Ori
    •  & Robert Tampé

  • Article
    | Open Access

    Initiation factor eIF2, common to eukaryotes and archaea, is a central actor in translation initiation. Here the authors describe two cryo-EM structures of archaeal 30S initiation complexes that provide a novel view of the central role that e/aIF2 plays in start codon selection.

    • Pierre-Damien Coureux
    • , Christine Lazennec-Schurdevin
    •  & Yves Mechulam

  • Article
    | Open Access

    Leishmania donovani is a protozoan parasite that can cause fatal infections in humans. Here the authors present a high resolution cryoEM structure of the L. donovani80S ribosome and compare it to its human counterpart to provide insight into the basis for drug selectivity towards this eukaryotic parasite.

    • Xing Zhang
    • , Mason Lai
    •  & Z. Hong Zhou

  • Article
    | Open Access

    Type IV pili are present on a wide range of bacterial pathogens and mediate diverse functions. Here the authors report a high resolution crystal structure of the pilin subunit PilE, and a cryoEM reconstruction of the Type IV pilus filament from N. meningitidisthat offer insight into pilus assembly and functions.

    • Subramania Kolappan
    • , Mathieu Coureuil
    •  & Lisa Craig

  • Article
    | Open Access

    The β-barrel assembly machinery (BAM complex) is a key mediator of outer membrane protein biogenesis in Gram-negative bacteria. Here the authors report a cryo-EM structure of the intact BAM complex that suggests that lateral gate opening is a necessary part of the BAM functional cycle.

    • Matthew G. Iadanza
    • , Anna J. Higgins
    •  & Neil A. Ranson

  • Article
    | Open Access

    The ribosome of bacteria and other unicellular pathogens is a common target for antibiotic drugs. Here the authors determine a structure of the human ribosome bound to the translation inhibitor cycloheximide, and provide evidence that targeting the ribosome is a promising avenue for cancer therapy.

    • Alexander G. Myasnikov
    • , S. Kundhavai Natchiar
    •  & Bruno P. Klaholz

  • Article
    | Open Access

    MS2 is a single-stranded RNA bacteriophage that infects its host via adsorption to bacterial pili. Here the authors visualize the MS2 virion with asymmetric cryo-EM reconstruction, revealing that the genome of MS2 adopts a specific structure of asymmetrically distributed stem-loops connected to the capsid.

    • Roman I Koning
    • , Josue Gomez-Blanco
    •  & Abraham J. Koster

  • Article
    | Open Access

    Prokaryotic translation initiation involves mRNA-ribosomal RNA base pairing interactions. Here, the authors provide evidence for a similar base pairing interactions occurring between the human h4 mRNA and helix 16 of the small subunit rRNA to position the correct AUG codon in the decoding site.

    • Franck Martin
    • , Jean-François Ménétret
    •  & Gilbert Eriani

  • Article
    | Open Access

    Cohesin is a ring-shaped protein complex that structures chromatin and mediates sister chromatid cohesion. Here the authors rigidify cohesin using engineered Smc1 and Smc3 and generated 3D models showing how Pds5B forms an integral part of the cohesin ring.

    • Michael T. Hons
    • , Pim J. Huis in ‘t Veld
    •  & Jan-Michael Peters

  • Article
    | Open Access

    Aerolysin is a secreted bacterial pore forming toxin that inserts into the host plasma membrane, potentially leading to cell death. Here the authors present Cryo-EM structures of aerolysin arrested at different stages of the pore formation process that provide insight into the conformational changes that allow pore formation.

    • Ioan Iacovache
    • , Sacha De Carlo
    •  & Benoît Zuber

  • Article
    | Open Access

    When the antibiotic erythromycin is bound to the ribosomal exit tunnel, ErmBL peptide translation stalls and allows translation of the downstream methyltransferase ErmB. Here the authors combine cryo-EM and molecular dynamics simulations to identify the underlying basis for the inhibition of peptide bond formation that results in ribosome stalling.

    • Stefan Arenz
    • , Lars V. Bock
    •  & Daniel N. Wilson

  • Article
    | Open Access

    Lysenin is member of the aerolysin family of small ß-barrel pore-forming toxins that include virulence factors from several human and animal pathogens. Here the authors determine the structure of the lysenin pore by single particle cryo- EM and propose a conserved pore formation mechanism for the aerolysin protein family.

    • Monika Bokori-Brown
    • , Thomas G. Martin
    •  & Christos G. Savva

  • Article
    | Open Access

    Transient receptor potential (TRP) proteins are Ca2+-permeable cation channels activated by a range of chemical and physical stimuli. Here the authors describe a cryo-EM structure of the full-length TRPV2 channel that provides insight into the regulation of the TRPV subfamily of channels.

    • Kevin W. Huynh
    • , Matthew R. Cohen
    •  & Vera Y. Moiseenkova-Bell

  • Article
    | Open Access

    Use of electron microscopy to determine morphology, or find where functionally significant biomolecules are located with high spatial resolution is of great interest. Here, Rez, Cohen et al. use aloof electron beam vibrational spectroscopy to probe different bonds in biological samples with no significant radiation damage.

    • Peter Rez
    • , Toshihiro Aoki
    •  & Hagai Cohen

  • Article
    | Open Access

    The Cdc45-MCM-GINS (CMG) helicase unwinds DNA during replication, a process that requires the ATPase-dependent activity of the MCM complex. Using cryo-EM reconstructions of the CMG complex in different conformations, the authors propose a model where the N-terminal and AAA+ domains of MCM work in concert to translocate along DNA.

    • Ferdos Abid Ali
    • , Ludovic Renault
    •  & Alessandro Costa

  • Article
    | Open Access

    Although the resolution achievable with cryo-EM can now rival crystallography, its application to small protein assemblies remains challenging. Here the authors demonstrate the use of the Volta phase plate for single particle analysis and its potential for the study of small specimens.

    • Maryam Khoshouei
    • , Mazdak Radjainia
    •  & Radostin Danev

  • Article
    | Open Access

    CCR4-NOT is a protein complex involved in a variety of important genetic processes. Here, the authors report the mid-resolution structure of this complex, and model the positions and contacts between the subunits, providing structural support for the previously reported functions of the complex.

    • Marta Ukleja
    • , Jorge Cuellar
    •  & Jose M. Valpuesta

  • Article
    | Open Access

    Bacterial type III secretion systems (T3SSs) inject virulence effector proteins into eukaryotic cells and are activated by host membrane contact. Here the authors report the in situ structure of the Chlamydia trachomatisT3SS in the presence or absence of host membrane, and observe compaction of the basal body embedded in the bacterial envelope.

    • Andrea Nans
    • , Mikhail Kudryashev
    •  & Richard D. Hayward

  • Article
    | Open Access

    Dispersed lipid self-assembly can form various types of particles, including cubosomes, which are useful for drug delivery. Here, Demurtas et al. visualize their three-dimensional structure, showing two continuous water channels separated by lipid bilayers and the mechanism of particle stabilization.

    • Davide Demurtas
    • , Paul Guichard
    •  & Laurent Sagalowicz

  • Article
    | Open Access

    Large-scale dense reconstruction of neuronal circuits (or connectomics) requires methods for large-volume dense en-blocelectron microscopy (EM) staining. Here the authors develop a protocol for staining tissue blocks from mouse neocortex sized at least 1 mm in diameter, enabling correlated functional and structural circuit analyses.

    • Yunfeng Hua
    • , Philip Laserstein
    •  & Moritz Helmstaedter

  • Article
    | Open Access

    The Hepatitis C virus (HCV) relies on an internal ribosome entry site (IRES) for translation of all the proteins encoded by its single-stranded RNA genome. Here the authors present a near-atomic cryo-EM structure of the HCV IRES bound to the human ribosome, shedding light on the initiation mechanism of HCV's and related IRESs.

    • Nick Quade
    • , Daniel Boehringer
    •  & Nenad Ban

  • Article
    | Open Access

    Tailed bacteriophages translocate the genome into and out of the capsid through a portal protein assembly located between the phage s head and tail. Here Sun et al. provide a cryo-EM structure of the bacteriophage T4 portal protein assembly, suggesting the functions and evolution of the portal structure.

    • Lei Sun
    • , Xinzheng Zhang
    •  & Michael G. Rossmann

  • Article
    | Open Access

    The proteasome is a highly regulated complex fundamental for cell homeostasis and a target for cancer therapy. Here the authors use cryo-EM and single-particle analysis to obtain a detailed map of the interactions between each active sites of the core 20S proteasome and the irreversible inhibitor AdaAhx3L3VS.

    • Paula C.A. da Fonseca
    •  & Edward P. Morris

  • Article
    | Open Access

    Preparing biological material for electron microscopy (EM) involves harsh processing steps that can poorly preserve cellular ultrastructure. Here the authors apply a single layer of graphene onto wet cells to enable direct EM using low voltage, and correlate actin filaments and mitochondria using super-resolution microscopy.

    • Michal Wojcik
    • , Margaret Hauser
    •  & Ke Xu

  • Article |

    While the cytosolic translation machinery is well characterized, the mitochondrial translation system remains largely elusive. Using cryo-electron tomography, Pfeffer et al. describe the ordered organization of mitochondrial polysomes in which each ribosome is tethered to the inner membrane by two defined contacts on the large subunit in situ.

    • Stefan Pfeffer
    • , Michael W. Woellhaf
    •  & Friedrich Förster

  • Article |

    Solving structures of large protein complexes remains a significant challenge for structural biologists. Demers et al. determine the atomic structure of a Shigellatype-III secretion system using a Rosetta-based modelling strategy that draws on both solid-state NMR and cryo-electron microscopy data sets.

    • Jean-Philippe Demers
    • , Birgit Habenstein
    •  & Nikolaos G. Sgourakis

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