Electron microscopy articles within Nature Communications

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  • Article
    | Open Access

    The COP9 signalosome (CSN) regulates Cullin-RING Ligase 2 (CRL2) but the molecular basis for their interaction is unknown. Here the authors use structural mass spectrometry and cryo-EM approaches to assess the structures and dynamics of CSN-CRL2 complexes.

    • Sarah V. Faull
    • , Andy M. C. Lau
    •  & Argyris Politis

  • Article
    | Open Access

    Set2 methyltransferase catalyzes the lysine 36 methylation of histone H3 (H3K36me) and the enzyme is mutated in many cancers. The authors provide mechanistic insights into how Set2 methylates nucleosomes by determining the 3.8 Å cryo-EM structure of Set2 bound to a H2B ubiquitinated nucleosome core particle.

    • Silvija Bilokapic
    •  & Mario Halic

  • Article
    | Open Access

    The Src-homology 3 domain of phosphatidyl-inositol-3-kinase (PI3K-SH3) is a model system for studying amyloid fibril formation. Here the authors present the 3.4 Å cryo-EM structure of the PI3K-SH3 amyloid fibril, which allows them to rationalize the effects of mutations on the kinetics of fibril formation.

    • Christine Röder
    • , Nicola Vettore
    •  & Gunnar F. Schröder

  • Article
    | Open Access

    Multiple adeno-associated viruses (AAV) use the same receptor (AAVR), but the binding mode is not clear. Here, the authors determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, identify residues necessary for virus entry and compare the receptor interfaces of different AAV capsids.

    • Ran Zhang
    • , Guangxue Xu
    •  & Zhiyong Lou

  • Article
    | Open Access

    The transient receptor potential channel member 2 (TRPM2) ion channel has a function in redox-dependent signaling. Here the authors present the cryo-EM structures of zebrafish TRPM2 in the ligand-free form, with Ca2+ and both ADP-ribose/Ca2+ and observe two-fold symmetric quaternary structure rearrangements in the ligand-bound structures that likely represent intermediate gating states.

    • Ying Yin
    • , Mengyu Wu
    •  & Seok-Yong Lee

  • Article
    | Open Access

    The genome of double-stranded DNA bacteriophages is delivered to host cells through the viral portal and tail structures. Here the authors describe structures of the bacteriophage T7 portal and the 1.5 MDa tail complex formed by the portal protein, adaptor protein and nozzle, providing insight into how the portal and tail machinery work during DNA packaging and ejection.

    • Ana Cuervo
    • , Montserrat Fàbrega-Ferrer
    •  & Miquel Coll

  • Article
    | Open Access

    How the human Alanine Serine Cysteine Transporter 2 (ASCT2) binds its substrates, neutral amino acids, and releases them on the cytoplasmic side remains unclear. Here authors present an inward-open structure of the human ASCT2 which shows that a hairpin serves as a gate in the inward-facing state.

    • Alisa A. Garaeva
    • , Albert Guskov
    •  & Cristina Paulino

  • Article
    | Open Access

    In patients with sporadic Alzheimer’s disease part of the Asp23 residues are isomerized to L-isoaspartate (L-isoAsp23). Here the authors present the MicroED structures of wild-type and L-isoAsp23 Aβ 20–34 amyloid fibrils that both form tightly packed cores and self-associate through two distinct interfaces with one of these interfaces being strengthened by the isoaspartyl modification.

    • Rebeccah A. Warmack
    • , David R. Boyer
    •  & Steven G. Clarke

  • Article
    | Open Access

    Torsins are unusual AAA + ATPases of unknown function that reside in the endoplasmic reticulum of all animals. Here the authors report that TorsinA forms tubular helical filaments with an unusual periodicity and that filamentous TorsinA directly interacts with membranes to form tubular protrusions.

    • F. Esra Demircioglu
    • , Weili Zheng
    •  & Thomas U. Schwartz

  • Article
    | Open Access

    Serotonin receptors (5-HT3R) belong to the pentameric ligand-gated ion channel superfamily and mediate excitatory postsynaptic signaling. Here the authors present the high-resolution cryo-EM structure of 5-HT3AR bound with the competitive antagonist granisetron and further validate the granisetron-binding mode with electrophysiology measurements and MD simulations.

    • Sandip Basak
    • , Yvonne Gicheru
    •  & Sudha Chakrapani

  • Article
    | Open Access

    Single-stranded RNA bacteriophages use a single maturation protein (Mat) to attach to a retractile pilus of the bacterial host. Here, the authors report the structures of the MS2 phage bound to the host receptor F-pili and define the orientations of Mat relative to the cell and emanating F-pili, providing new insights into the F-like type IV secretion systems.

    • Ran Meng
    • , Mengqiu Jiang
    •  & Junjie Zhang

  • Article
    | Open Access

    Bacteriophages reprogram the host transcriptional machinery. Here the authors provide insights into the mechanism of how bacteriophages regulate host transcription by determining the cryo-EM structures of two bacterial transcription elongation complexes bound with the bacteriophage master host-transcription regulator protein P7.

    • Linlin You
    • , Jing Shi
    •  & Yu Zhang

  • Article
    | Open Access

    CARD9 and CARD11 propagate signaling by nucleating Bcl10 polymerization in immune cells and are both held in an autoinhibited state prior to activation. Here, the authors combine structural, biochemical, and cell-based approaches to reveal the structural basis for CARD9/11 autoinhibition and show that the two proteins are activated through similar but distinct mechanisms.

    • Michael J. Holliday
    • , Axel Witt
    •  & Wayne J. Fairbrother

  • Article
    | Open Access

    McrBC is a bacterial antiphage defense system that cleaves methylated DNA and is composed of the AAA+ GTPase motor McrB and the endonuclease McrC. Here, the authors present the cryo-EM structure of E. coli McrBC that reveals how McrC inserts a stalk-like structure into the pore of the ring-shaped McrB hexamer and discuss mechanistic implications.

    • Neha Nirwan
    • , Yuzuru Itoh
    •  & Kayarat Saikrishnan

  • Article
    | Open Access

    Lamin A is critical for nuclear architecture but its structure and assembly are not fully understood. Here, the authors use quantitative cross-linking mass spectrometry to map intra- and intermolecular interactions within lamin homomers, providing insights into the molecular basis for lamin’s mechanical properties.

    • Alex A. Makarov
    • , Juan Zou
    •  & Eric C. Schirmer

  • Article
    | Open Access

    Type III CRISPR-Cas systems are able to target transcriptionally active DNA sequences in phages and plasmids. Here, the authors reveal the mechanism of the target nucleic acid preference of Type III-A CRISPR-Cas complexes at the transcription bubble by a combination of structural and biochemical approaches.

    • Tina Y. Liu
    • , Jun-Jie Liu
    •  & Jennifer A. Doudna

  • Article
    | Open Access

    Coral fossils can record climatic history, but teasing apart environmental signals remains a challenge. Here the authors show that crystallographic changes in coral skeletons grown under high CO2 conditions could be used as a sensitive pH proxy, enabling measurement of ocean acidification back in time.

    • Ismael Coronado
    • , Maoz Fine
    •  & Jarosław Stolarski

  • Article
    | Open Access

    The NER machinery contains the multisubunit transcription factor IIH (TFIIH) that opens the DNA repair bubble, scans for the lesion, and coordinates excision of the damaged site. Here the authors resolve the cryo-electron microscopy structure of the human core TFIIH-XPA-DNA complex and provide insights into its activation.

    • Goran Kokic
    • , Aleksandar Chernev
    •  & Patrick Cramer

  • Article
    | Open Access

    β-propeller domains are an important class of folding substrates for the eukaryotic cytosolic chaperonin CTT. Here the authors find that CTT contributes to the folding and assembly of two β-propeller proteins from mTOR complexes, mLST8 and Raptor, and determine the 4.0 Å cryoEM structure of a human mLST8-CCT intermediate that shows mLST8 in a near-native state.

    • Jorge Cuéllar
    • , W. Grant Ludlam
    •  & José M. Valpuesta

  • Article
    | Open Access

    Proteins are translocated across membranes through the Sec61/SecY channel. Here, the authors present the structure of a translocating peptide chain trapped inside the SecA-SecY complex which suggests how peptides are actively moved through the channel.

    • Chengying Ma
    • , Xiaofei Wu
    •  & Long Li

  • Article
    | Open Access

    The plasmid-segregating actin-like protein ParM is encoded on the large, toxin carrying plasmid pCBH from Clostridium botulinum. Here the authors present the cryo-EM structure of the ParM filament that is formed from the association of 15 protofilaments and discuss its architecture.

    • Fujiet Koh
    • , Akihiro Narita
    •  & Robert C. Robinson

  • Article
    | Open Access

    NMR structure determination is challenging for proteins with a molecular weight above 30 kDa and atomic-resolution structure determination from cryo-EM data is currently not the rule. Here the authors describe an integrated structure determination approach that simultaneously uses NMR and EM data and allows them to determine the structure of the 468 kDa dodecameric aminopeptidase TET2 complex.

    • Diego F. Gauto
    • , Leandro F. Estrozi
    •  & Jerome Boisbouvier

  • Article
    | Open Access

    Multidrug efflux pumps actively expel a wide range of toxic substrates from bacteria and play a major role in drug resistance. Here authors show the in situ structure of the efflux pump AcrAB-TolC obtained by electron cryo-tomography and subtomogram averaging.

    • Xiaodong Shi
    • , Muyuan Chen
    •  & Zhao Wang

  • Article
    | Open Access

    During stress, protein synthesis is inhibited through phosphorylation of the initiation factor eIF2 on its alpha subunit and its interaction with eIF2B. Here the authors describe a structure of the yeast eIF2B in complex with its substrate - the GDP-bound phosphorylated eIF2, providing insights into how phosphorylation results in a tighter interaction with eIF2B.

    • Yuliya Gordiyenko
    • , José Luis Llácer
    •  & V. Ramakrishnan

  • Article
    | Open Access

    Epsilon toxin (Etx) is a potent pore forming toxin (PFT) produced by Clostridium perfringens. Here authors show the cryo-EM structure of the Etx pore assembled on the membrane of susceptible cells and shed light on pore formation and mutant phenotypes.

    • Christos G. Savva
    • , Alice R. Clark
    •  & Monika Bokori-Brown

  • Article
    | Open Access

    Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides, which is an essential step in DNA synthesis. Here the authors use small-angle X-ray scattering, X-ray crystallography, and cryo-electron microscopy to capture active and inactive forms of the Bacillus subtilis RNR and provide mechanistic insights into a convergent form of allosteric regulation.

    • William C. Thomas
    • , F. Phil Brooks III
    •  & Nozomi Ando

  • Article
    | Open Access

    Ribonulease P is a conserved ribozyme present in all kingdoms of life that is involved in the 5′ maturation step of tRNAs. Here the authors determine the structure of an archaeal RNase P holoenzyme that reveals how archaeal RNase P recognizes its tRNA substrate and suggest a conserved catalytic mechanism amongst RNase Ps despite structural variability.

    • Futang Wan
    • , Qianmin Wang
    •  & Ming Lei

  • Article
    | Open Access

    Translation termination is under strong selection pressure for high speed and accuracy. Here the authors provide a 3D view of the dynamics of a translating bacterial ribosome as it recruits a class-1 release factor (RF1 or RF2) upon encountering a stop codon, and propose a structure-based kinetic model for the early steps in bacterial translation termination.

    • Ziao Fu
    • , Gabriele Indrisiunaite
    •  & Joachim Frank

  • Article
    | Open Access

    The neuronal Ca2+-sensor Synapotagmin-1 (Syt1) interacts with SNARE proteins and lipid membranes and synchronizes neurotransmitter release in response to Ca2+-influx. Here the authors provide insights into the underlying molecular mechanism by determining the cryo-EM structure of the Syt1–SNARE complex on a lipid membrane at 10 Å resolution.

    • Kirill Grushin
    • , Jing Wang
    •  & Shyam S. Krishnakumar

  • Article
    | Open Access

    Bacterial ClpB is a disaggregase that solubilizes protein aggregates. Here the authors present the 2.9 Å cryo-EM structure of a hyperactive variant of ClpB bound to the substrate casein in active translocation states and discuss its polypeptide translocation mechanism.

    • Alexandrea N. Rizo
    • , JiaBei Lin
    •  & Daniel R. Southworth

  • Article
    | Open Access

    Mature particles of bacteriophage ϕ29 consist of a 33-MDa complex formed by over 450 subunits, assembled into a head and a short tail. Here, Xu et al. report the near-atomic structures of the ϕ29 prohead, the mature virion and the genome-emptied virion, providing insights into DNA packaging and release.

    • Jingwei Xu
    • , Dianhong Wang
    •  & Ye Xiang

  • Article
    | Open Access

    The pathogenic human coronaviruses SARS- and MERS-CoV can cause severe respiratory disease. Here the authors present the 3.1Å cryo-EM structure of the SARS-CoV RNA polymerase nsp12 bound to its essential co-factors nsp7 and nsp8, which is of interest for antiviral drug development.

    • Robert N. Kirchdoerfer
    •  & Andrew B. Ward

  • Article
    | Open Access

    CENP-A histone variants replace histones H3 at centromeres. Here the authors use a single-chain antibody fragment (scFv) to stabilize human CENP-A nucleosome containing a native α-satellite DNA and solved its structure by cryo-EM to 2.6 Å resolution, providing insight into the structure and function of the CENP-A nucleosome.

    • Bing-Rui Zhou
    • , K. N. Sathish Yadav
    •  & Ping Zhang

  • Article
    | Open Access

    Hedgehog (Hh) controls embryonic development via interaction with its receptor Patched (Ptch). Here the authors report the cryo-EM structure of tetrameric Ptch1 in complex with the palmitoylated N-terminal signaling domain of human Sonic hedgehog (ShhNp) at a 4:2 stoichiometric ratio.

    • Hongwu Qian
    • , Pingping Cao
    •  & Xin Gong

  • Article
    | Open Access

    Rotaviruses are of great medical significance because they cause gastroenteritis in children. Here the authors provide insights into the mechanism of viral mRNA transcription by determining the in situ cryo-EM structures of a working rotavirus’ RNA-dependent-RNA polymerase, which is of interest for antiviral drug design.

    • Ke Ding
    • , Cristina C. Celma
    •  & Z. Hong Zhou

  • Article
    | Open Access

    During the integrated stress response, translation is modulated through the phosphorylation of translation initiation factor eIF2 and the formation of a complex with eIF2B. Here the authors present structures of the eIF2:eIF2B complex with and without phosphorylation, shedding light on how eIF2 phosphorylation regulates translation.

    • Tomas Adomavicius
    • , Margherita Guaita
    •  & Graham D. Pavitt

  • Article
    | Open Access

    YenTcA is the pore-forming and membrane binding subunit of the ABC toxin YenTc, which is produced by the insect pathogen Yersinia entomophaga. Here authors present cryo-EM structures of YenTcA purified from the native source which implicate associated endochitinases in host cell recognition.

    • Sarah J Piper
    • , Lou Brillault
    •  & Michael J Landsberg

  • Article
    | Open Access

    Proteins smaller than about 50 kDa are currently too small to be imaged at high resolution by cryo‐electron microscopy (cryo‐EM). Here authors design a protein scaffold that binds 12 copies of a small 26 kDa protein (GFP), which allowed visualizing GFP at a resolution of 3.8Å by cryo‐EM.

    • Yuxi Liu
    • , Duc T. Huynh
    •  & Todd O. Yeates

  • Article
    | Open Access

    2D crystals of the MloK1 potassium channel diffract to only 10 Å. Here the authors present a method, where they apply cryo-EM single-particle image processing to recorded 2D crystal images, which reveals conformational conformational variability of MloK1 within the crystals and enabled them to determine the structure at 4 Å resolution.

    • Ricardo D. Righetto
    • , Nikhil Biyani
    •  & Henning Stahlberg

  • Article
    | Open Access

    Bacteria use contractile injection systems, such as type VI secretion systems (T6SS), to secrete proteins that mediate cell-cell interactions. Here, Szwedziak & Pilhofer show that both ends of a T6SS can attach to opposite sides of the cell, enabling the structure to contract in two opposite directions.

    • Piotr Szwedziak
    •  & Martin Pilhofer

  • Article
    | Open Access

    Here, the authors present the cryo-EM structure of the archaeal virus SH1 at 3.8 Å resolution and show how the major capsid proteins assemble into hetero-hexamers, providing insights into the assembly process of this and related PRD1-adeno lineage viruses.

    • Luigi De Colibus
    • , Elina Roine
    •  & David I. Stuart

  • Article
    | Open Access

    Here, the authors present the cryo-EM structures of two archaeal, halophilic, internal membrane-containing icosahedral viruses at 3.7 and 3.8 Å resolution, providing insights into the assembly process of these and related PRD1-adeno lineage viruses.

    • Isaac Santos-Pérez
    • , Diego Charro
    •  & Nicola G. A. Abrescia

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