Electron microscopy articles within Nature Communications

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  • Article
    | Open Access

    The pathogen recognition receptors NOD1/2 recognize bacterial cell wall components and signal through their downstream adapter kinase RIP2 via a CARD (Caspase activation and recruitment domain) mediated oligomerization process. Here the authors present the cryo-EM structure of the active RIP2-CARD filament and discuss implications for NOD1/2-RIP2 signalling.

    • Qin Gong
    • , Ziqi Long
    •  & Bin Wu

  • Article
    | Open Access

    Transcription preinitiation complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID complex, providing a detailed view of its subunit organization and promoter DNA contacts.

    • Olga Kolesnikova
    • , Adam Ben-Shem
    •  & Gabor Papai

  • Article
    | Open Access

    Impaired kidney function can lead to an increase of β2-microglobulin (β2m) serum levels, which can cause β2m aggregation and amyloid fibril formation. Here the authors combine cryo-EM and magic angle spinning NMR measurements to determine the structure of a β2m fibril and they also present the low resolution model of a β2m fibril with a different morphology.

    • Matthew G. Iadanza
    • , Robert Silvers
    •  & Sheena E. Radford

  • Article
    | Open Access

    The insulin receptor plays a key role in many physiological processes, yet how insulin effects receptor signaling at the structural level remains incomplete. Here the authors present a high-resolution cryo-EM structure of a high-affinity form of the insulin-bound insulin receptor ectodomain that sheds light on the mechanism of signal transduction.

    • Felix Weis
    • , John G. Menting
    •  & Michael C. Lawrence

  • Article
    | Open Access

    Enzymes of the six-transmembrane epithelial antigen of the prostate (STEAP) family reduce Fe3+ and Cu2+ ions to facilitate metal-ion uptake by mammalian cells. Here, authors employ single-particle cryo-EM to gain insights into the molecular principles of iron reduction by human STEAP4 .

    • Wout Oosterheert
    • , Laura S. van Bezouwen
    •  & Piet Gros

  • Article
    | Open Access

    TRPV5 is a kidney specific transient receptor potential (TRP) channel with an important role in calcium reabsorption. Here the authors provide mechanistic insights into TRPV5 modulation by determining the phosphatidylinositol 4,5-bisphosphate and calmodulin bound TRPV5 cryo-EM structures.

    • Taylor E. T. Hughes
    • , Ruth A. Pumroy
    •  & Vera Y. Moiseenkova-Bell

  • Article
    | Open Access

    During stress conditions bacterial ribosomes dimerize and form inactive but stable hibernating 100S particles, a process that is facilitated by the hibernation-promoting factor (HPF). Here the authors analyze 100S dimer formation as a function of HPF protein concentration and present the Thermus thermophilus 100S ribosome cryo-EM structure.

    • Rasmus Kock Flygaard
    • , Niels Boegholm
    •  & Lasse B. Jenner

  • Article
    | Open Access

    The COPII coat assembles in two concentric layers and mediates protein export from the endoplasmic reticulum. Here the authors present the 4.9 Å resolution cryo-tomography and subtomogram averaging structure of the membrane bound COPII inner coat that was obtained by in vitro reconstitution and discuss mechanistic implications.

    • Joshua Hutchings
    • , Viktoriya Stancheva
    •  & Giulia Zanetti

  • Article
    | Open Access

    The BCL10-MALT1 complex is a central signaling hub in lymphocytes and linked to various human immune pathologies. Here the authors present the cryo-EM structure of the BCL10-MALT1 filament core and verify the identified BCL10/MALT1 interface with mutagenesis studies.

    • Florian Schlauderer
    • , Thomas Seeholzer
    •  & Katja Lammens

  • Article
    | Open Access

    Binding of bacterial peptidoglycan muramyl dipeptides induces NOD2 activation and signalling via the downstream adaptor kinase RIP2. Here the authors show that RIP2 forms filaments via its CARD domain, analyse the structure of the CARD filaments and demonstrate the requirement of RIP2 polymerisation for the activation of NF-κB by NOD2.

    • Erika Pellegrini
    • , Ambroise Desfosses
    •  & Stephen Cusack

  • Article
    | Open Access

    The type-I fatty acid synthase (FAS-I) complex is essential for Mycobacterium tuberculosis (Mtb) and mediates the production of C26 fatty acids that are precursors for the synthesis of mycolic acids. Here the authors present the 3.3 Å resolution cryo-EM structure of Mtb FAS-I, which is of interest for tuberculosis drug development.

    • Nadav Elad
    • , Szilvia Baron
    •  & Ron Diskin

  • Article
    | Open Access

    The bacterial type III secretion system of Gram-negative bacteria uses its core, the needle complex, to penetrate through the infected host cell membrane. Here authors show a near-atomic resolution structure of a needle complex which sheds light on the assembly and function of this nanomachine.

    • J. Hu
    • , L. J. Worrall
    •  & N. C. J. Strynadka

  • Article
    | Open Access

    The determination of high resolution structures of G protein coupled receptors (GPCRs) in complex with heterotrimeric G proteins is challenging. Here authors develop an antibody fragment, mAB16, which stabilizes GPCR/G-protein complexes and facilitates the application of high resolution cryo-EM.

    • Shoji Maeda
    • , Antoine Koehl
    •  & Brian K. Kobilka

  • Article
    | Open Access

    Herpes simplex virus type-2 (HSV-2) belongs to the α-herpesvirinae subfamily and is a sexually transmitted virus that causes genital ulcer disease. Here the authors present the 3.75 Å cryo-EM structure of the HSV-2 C-capsid with capsid-vertex-specific component and describe α-herpesvirus-specific structural features.

    • Jialing Wang
    • , Shuai Yuan
    •  & Xiangxi Wang

  • Article
    | Open Access

    Single-particle cryo-EM is a powerful method for macromolecular structure determination. Here the authors demonstrate that Ewald sphere curvature correction, sub-Angstrom pixilation and per-particle CTF refinement can improve map quality and resolution and present the 1.86 Å cryo-EM structure of an adeno-associated virus serotype 2 variant.

    • Yong Zi Tan
    • , Sriram Aiyer
    •  & Dmitry Lyumkis

  • Article
    | Open Access

    The plasma membrane Ca2+ ATPase (PMCA) is essential for maintaining Ca2+ homeostasis in eukaryotic cells, and neuroplastin (NPTN) was recently identified as an obligatory subunit of PMCA. Here the authors present the cryo-EM structure of NPTN bound to human PMCA1, which reveals that the NPTN transmembrane (TM) helix interacts with TM10 and the TM8-9-linker of PMCA1.

    • Deshun Gong
    • , Ximin Chi
    •  & Qiang Zhou

  • Article
    | Open Access

    Only a few archaeal filamentous viruses have been structurally characterized. Here the authors describe the membrane-enveloped Sulfolobus filamentous virus 1 that infects Sulfolobus shibatae and present its 3.7 Å resolution cryo-EM structure, which reveals that major coat proteins are structurally conserved among archaeal filamentous viruses.

    • Ying Liu
    • , Tomasz Osinski
    •  & Edward H. Egelman

  • Article
    | Open Access

    The Complement component 9 (C9) is the pore-forming component of the Membrane Attack Complex which targets pathogens. Here authors use structural biology to compare monomeric C9 to C9 within the polymeric assembly and identify the element which inhibits C9 self-assembly in the absence of the target membrane.

    • Bradley A. Spicer
    • , Ruby H. P. Law
    •  & Michelle A. Dunstone

  • Article
    | Open Access

    Members of the transient receptor potential (TRP) ion channels conduct cations into cells upon activation by a variety of signals. Here authors present the cryo-EM structure of TRPC4 in its unliganded (apo) state, which provides molecular insights into TRPC4's ion selectivity and TPR channel evolution.

    • Jingjing Duan
    • , Jian Li
    •  & Jin Zhang

  • Article
    | Open Access

    The transient receptor potential channel TRPV6 mediates calcium uptake in epithelia and its expression is increased in several cancer types. Here, authors present structures of TRPV6 bound to 2-APB, a TRPV6 inhibitor, and show that 2-APB induces TRPV6 channel closure by modulating protein–lipid interactions.

    • Appu K. Singh
    • , Kei Saotome
    •  & Alexander I. Sobolevsky

  • Article
    | Open Access

    Geminiviruses are an important plant pathogen that causes large food crop losses globally. Here the authors describe a high resolution cryo-EM structure of the Ageratum yellow vein virus and reveal the molecular details of how a single capsid protein sequence can adopt the different conformations needed to build that geminate capsid.

    • Emma L. Hesketh
    • , Keith Saunders
    •  & Neil A. Ranson

  • Article
    | Open Access

    While the architecture of vertebrate nuclear pore complexes (NPCs) is well understood, the extent of its evolutionary conservation is still unclear. Here, the authors analyze the in situ architecture of an algal NPC, revealing distinct structural features that provide insights into NPC evolution.

    • Shyamal Mosalaganti
    • , Jan Kosinski
    •  & Martin Beck

  • Article
    | Open Access

    Mutations in the cation channel PKD2 cause human autosomal dominant polycystic kidney disease but its channel function and gating mechanism are poorly understood. Here authors study PKD2 using electrophysiology and cryo-EM, which identifies hydrophobic gates and proposes a gating mechanism for PKD2.

    • Wang Zheng
    • , Xiaoyong Yang
    •  & Xing-Zhen Chen

  • Article
    | Open Access

    Cofilin is a small actin-binding protein that accelerates actin turnover by disassembling actin filaments. Here the authors present the 3.8 Å cryo-EM structure of a cofilin-decorated actin filament and discuss mechanistic implications.

    • Kotaro Tanaka
    • , Shuichi Takeda
    •  & Akihiro Narita

  • Article
    | Open Access

    The Yersinia YaxAB system is a pore-forming toxin of so far unknown structure. Here authors present X-ray and cryo-EM to structures of individual subunits and of the YaxAB pore complex, and find that YaxA binds to membranes first and recruits YaxB for subsequent oligomerization.

    • Bastian Bräuning
    • , Eva Bertosin
    •  & Michael Groll

  • 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

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