Structural biology articles within Nature Communications

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  • Article
    | Open Access

    In Saccharomyces cerevisiae, unchecked proliferation of Ty1 retrotransposons is controlled by the process of copy number control (CNC), which requires the p22/p18 protein, translated from an internal transcript within the Ty1 GAG gene. Here, the authors present the 2.8 Å crystal structure of a minimal p18 from Ty1-Gag that is able to restrict Ty1 transposition and identify two dimer interfaces in p18, whose roles were probed by mutagenesis both in vitro and in vivo. As p22/p18 contains only one of two conserved domains required for retroelement Gag assembly, they propose that p22/p18-Gag interactions block the Ty1 virus-like particle assembly pathway, resulting in defective particles incapable of supporting retrotransposition.

    • Matthew A. Cottee
    • , Sean L. Beckwith
    •  & Ian A. Taylor

  • Article
    | Open Access

    C. elegans piRNA biogenesis and chromosome segregation (PICS) complex is composed of TOFU-6, PICS-1, ERH-2, and two mutually exclusive factors PID-1 and TOST-1. By employing biochemical, structural, and cellular biology methods, the authors show that the PICS complex is an octamer consisting of two copies of each subunit, and functions in piRNA biogenesis and mitosis.

    • Xiaoyang Wang
    • , Chenming Zeng
    •  & Chao Xu

  • Article
    | Open Access

    Epistasis plays an important role in the evolution of novel protein functions because it determines the mutational path a protein takes. Here, the authors combine functional, structural and biophysical analyses to characterize epistasis in a computationally redesigned ligand-inducible allosteric transcription factor and found that epistasis creates distinct biophysical and biological functional landscapes.

    • Kyle K. Nishikawa
    • , Nicholas Hoppe
    •  & Srivatsan Raman

  • Article
    | Open Access

    Replicative hexameric helicases are fundamental components of replisomes. Here the authors resolve a cryo-EM structure of the E1 helicase from papillomavirus bound to a DNA replication fork, providing insights into the mechanism of DNA unwinding by these hexameric enzymes.

    • Abid Javed
    • , Balazs Major
    •  & Elena V. Orlova

  • Article
    | Open Access

    Here, the authors present a hierarchical disorder model for the analysis of disorder in both crystal and cryo-EM structures. They apply their approach to several structures of three proteins, including SARS-CoV-2 proteins, and discuss mechanistic and dynamical implications.

    • Nicholas M. Pearce
    •  & Piet Gros

  • Article
    | Open Access

    Understanding the structural basis for the inhibition of archaeal eukaryotic-like RNA polymerases (RNAPs) during virus infection is of interest for drug design. Here, the authors present the cryo-EM structures of apo Sulfolobus acidocaldarius RNAP and the RNAP complex structures with two regulatory factors, RIP and TFS4 that inhibit transcription and discuss their inhibitory mechanisms.

    • Simona Pilotto
    • , Thomas Fouqueau
    •  & Finn Werner

  • Article
    | Open Access

    Here, cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion’s capsid-bound tegument protein, pp150. tRNA recruitment is mediated by the interactions specific for HCMV only, suggesting the explanation for the absence of such tRNA densities in related herpesviruses.

    • Yun-Tao Liu
    • , David Strugatsky
    •  & Z. Hong Zhou

  • Article
    | Open Access

    Soluble guanylate cyclase (sGC) is a validated drug target for cardiovascular diseases. Here, the authors report structures of human sGC in complex with NO and sGC stimulators or activator, providing insight into the mechanism of sGC activation by pharmacological compounds.

    • Rui Liu
    • , Yunlu Kang
    •  & Lei Chen

  • Article
    | Open Access

    Volume-regulated anion channels (VRACs) are heteromers of LRRC8 proteins, all containing the obligatory subunit LRRC8A. Here, the authors develop and characterize nanobodies that bind LRRC8A and allosterically modulate the function of homomeric LRRC8A and endogenous heteromeric channels, hinting at functional mechanisms present in VRACs.

    • Dawid Deneka
    • , Sonja Rutz
    •  & Raimund Dutzler

  • Article
    | Open Access

    OqxB is an RND (Resistance-Nodulation-Division) transporter that contributes to the antibiotic resistance in Klebsiella pneumoniae. Here, the authors report structural and functional characterization of OqxB, with insights into its substrate binding pocket and the role in fluoroquinolone resistance.

    • Nagakumar Bharatham
    • , Purnendu Bhowmik
    •  & Satoshi Murakami

  • Article
    | Open Access

    Dynamin mediates the fission of vesicles during endocytosis. Here, the authors report the cryoEM structure of a super-constricted two-start dynamin 1 filament- one of the two known helical forms of dynamin, with insights into the molecular mechanisms of dynamin-mediated membrane scission.

    • Jiwei Liu
    • , Frances Joan D. Alvarez
    •  & Peijun Zhang

  • Article
    | Open Access

    The large and small subunits of the ribosome are synthesized independently within the nucleolus — a membrane-less compartment within the nucleus — before being exported into the cytoplasm. Here, the authors use in situ cryo-ET to observe ribosome maturation and reveal the native organization of the nucleolus.

    • Philipp S. Erdmann
    • , Zhen Hou
    •  & Wolfgang Baumeister

  • Article
    | Open Access

    Bacteria adjust the expression of some of their metabolic enzymes through metabolite-sensing ribosome nascent chain complexes. Here the authors present a cryo-EM structure of an E. coli ribosome stalled during translation of the TnaC leader peptide and propose a model for L-Trp dependent ribosome stalling where L-Trp competes with release factor 2 for binding to the TnaC-ribosome complex.

    • Anne-Xander van der Stel
    • , Emily R. Gordon
    •  & C. Axel Innis

  • Article
    | Open Access

    The assembly of branched actin networks depends on the heterodimeric capping protein CP/CapZ. Combining cryoEM, in vitro reconstitution and cell biological assays, the authors show that CP not only prevents actin filament elongation but also selectively masks actin filament ends to promote nucleation.

    • Johanna Funk
    • , Felipe Merino
    •  & Peter Bieling

  • Article
    | Open Access

    Borosins are ribosomally encoded and posttranslationally modified peptide (RiPP) natural products featuring amide-backbone α-N-methylation. Here, the authors report the discovery and characterization of type IV borosin ‘split’ pathways encoding distinct, separate α-N-methyltransferases and precursor peptide substrates.

    • Fredarla S. Miller
    • , Kathryn K. Crone
    •  & Michael F. Freeman

  • Article
    | Open Access

    The endoplasmic-reticulum aminopeptidase ERAP1 processes peptides for antigen presentation. Here, the authors assess ERAP1 conformational states in solution, providing insight into the molecular mechanisms of ERAP1 substrate-length dependent catalytic activity and regulation, including the effects of autoimmune disease-associated polymorphism.

    • Zachary Maben
    • , Richa Arya
    •  & Lawrence J. Stern

  • Article
    | Open Access

    Here, the authors use solid-state NMR and EPR measurements to characterise the ATP hydrolysis transition state of the oligomeric bacterial DnaB helicase from Helicobacter pylori, which was trapped by using aluminium fluoride as a chemical mimic. They identify protein protons that coordinate to the phosphate groups of ADP and DNA and observe that the aluminium fluoride unit is highly mobile and fast-rotating.

    • Alexander A. Malär
    • , Nino Wili
    •  & Thomas Wiegand

  • Article
    | Open Access

    Elucidating specific effects of protein kinase Akt isoforms remains challenging. Here, the authors establish an Akt isoform-dependent cellular model system and use it, together with X-ray crystallography and structure-based ligand design, to develop isoform-selective covalent-allosteric Akt inhibitors

    • Lena Quambusch
    • , Laura Depta
    •  & Daniel Rauh

  • Article
    | Open Access

    Chimeric antigen receptor T cells in the clinic currently target cell-type-specific extracellular antigens on malignant cells. Here, authors engineer tumor-specific chimeric antigen receptor T cells that target human leukocyte antigen-presented neoantigens derived from mutant intracellular proteins.

    • Michael S. Hwang
    • , Michelle S. Miller
    •  & Sandra B. Gabelli

  • Article
    | Open Access

    The intrinsic disorder of histone tails poses challenges in their characterization. Here the authors apply extensive molecular dynamics simulations of the full nucleosome to show reversible binding to DNA with specific binding modes of different types of histone tails, where charge-altering modifications suppress tail-DNA interactions and may boost interactions between nucleosomes and nucleosome-binding proteins.

    • Yunhui Peng
    • , Shuxiang Li
    •  & Anna R. Panchenko

  • Article
    | Open Access

    The pyruvate dehydrogenase complex (PDHc) is a large multienzyme complex that converts pyruvate into acetyl-coenzyme A and in E. coli the core of the PDHc is formed by 24 copies of dihydrolipoyl transacetylase. Here, the authors present the cryo-EM structure of the E. coli dihydrolipoyl transacetylase 24-mer core in a native resting state including lipoyl domains, and discuss the mechanism of substrate shuttling by the lipoyl domains.

    • Jana Škerlová
    • , Jens Berndtsson
    •  & Pål Stenmark

  • Article
    | Open Access

    M. tuberculosis cytochrome bd oxidase is of interest as a TB drug target. Here, the authors present the 2.5 Å cryo-EM structure of M. tuberculosis cytochrome bd oxidase and identify a disulfide bond within the canonical quinol binding and oxidation domain (Q-loop) and a menaquinone-9 binding site at heme b595.

    • Schara Safarian
    • , Helen K. Opel-Reading
    •  & Hartmut Michel

  • Article
    | Open Access

    CD47 is a transmembrane receptor involved in the regulation of various signalling pathways and a promising target for immuno-oncology therapeutics. Here, the authors present the crystal structure of full-length human CD47 and provide insights into the molecular mechanism of CD47-mediated signalling.

    • Gustavo Fenalti
    • , Nicolas Villanueva
    •  & Kandasamy Hariharan

  • Article
    | Open Access

    m6A RNA post-transcriptional modification changes RNA hybridization kinetics. Here the authors show that the methylamino group can adopt syn-conformation pairing with uridine with a mismatch-like conformation in RNA duplex. They also develop a quantitative model that predicts how m6A affects the kinetics of hybridization.

    • Bei Liu
    • , Honglue Shi
    •  & Hashim M. Al-Hashimi

  • Article
    | Open Access

    ParA is an ATPase involved in the segregation of newly replicated DNA in bacteria. Here, structures of a ParA filament bound to DNA and of ParA in various nucleotide states offer insight into its conformational changes upon DNA binding and filament assembly, including the basis for ParA’s cooperative binding to DNA.

    • Alexandra V. Parker
    • , Daniel Mann
    •  & Julien R. C. Bergeron

  • Article
    | Open Access

    Epitopes formed by fusion of more than one self peptide, such as proinsulin and other β cell proteins, can result in the formation of non-self hybrid peptides that can potentially trigger autoimmune responses. Here the authors show how TRBV5 + T cell receptors are geared towards recognition of HLA-DQ8 bound hybrid peptides in patients with type 1 diabetes.

    • Mai T. Tran
    • , Pouya Faridi
    •  & Hugh H. Reid

  • Article
    | Open Access

    KdpFABC is a high-affinity bacterial K+ pump which combines the ion channel-like KdpA and the P-type ATPase KdpB. Here, the authors elucidate the mechanisms underlying transport and the coupling to ATP hydrolysis, and provide evidence that ions are transported via an intersubunit tunnel through KdpA and KdpB.

    • Jakob M. Silberberg
    • , Robin A. Corey
    •  & Inga Hänelt

  • Article
    | Open Access

    Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.

    • Hai Lei
    • , Quan Ma
    •  & Yi Cao

  • Article
    | Open Access

    Vilazodone (VLZ) is a drug for the treatment of major depressive disorders that targets the serotonin transporter (SERT). Here, the authors combine pharmacology measurements and cryo-EM structural analysis to characterize VLZ binding to SERT and observe that VLZ exhibits non-competitive inhibition of serotonin transport and binds with nanomolar affinity to an allosteric site in SERT.

    • Per Plenge
    • , Dongxue Yang
    •  & Claus J. Loland

  • Article
    | Open Access

    Ghrelin is a gastric peptide hormone and its acylation is required for binding to and activation of the ghrelin receptor in the brain, which initiates appetite. Here, the authors present cryo-EM structures of the Gq-coupled ghrelin receptor bound to ghrelin and the synthetic agonist GHRP-6 and they describe how the acylated peptide hormone is recognised by the receptor, which is of interest for drug design.

    • Yue Wang
    • , Shimeng Guo
    •  & Yi Jiang

  • Article
    | Open Access

    Understanding the structure and dynamics of enzymes is important for a number of applications. Here, the authors report on the crystal structure of vanillic acid decarboxylase, and show how the dynamics of the UbiD superfamily enzymes relate to the covalent catalysis of aromatic (de)carboxylation.

    • Stephen A. Marshall
    • , Karl A. P. Payne
    •  & David Leys

  • Article
    | Open Access

    Micro-crystal electron diffraction (MicroED) has shown great potential for the structure determination of crystals that are too small for X-ray diffraction but MicroED sample preparation remains challenging. Here, the authors present Preassis, a pressure-assisted method for the preparation of MicroED specimens and demonstrate that Preassis can be applied to a wide range of protein crystal suspensions with low and high viscosities, as well as those with low crystal concentrations.

    • Jingjing Zhao
    • , Hongyi Xu
    •  & Xiaodong Zou

  • Article
    | Open Access

    The rhoptry is an apical secretory organelle of apicomplexan parasites that is essential for host cell invasion. Here, Mageswaran et al. provide in situ ultrastructures of rhoptries from two pathogens, revealing a conserved architecture including luminal filaments and a distinct docking mechanism.

    • Shrawan Kumar Mageswaran
    • , Amandine Guérin
    •  & Yi-Wei Chang

  • Article
    | Open Access

    Bone morphogenetic protein (BMP) receptors are single pass transmembrane serine/threonine kinases that form tetrameric complexes comprised of two type I and two type II BMP receptors. Here the authors characterize a structure of an active type I/type II kinase tetramer providing insight into molecular mechanism driving ligand-induced signaling.

    • Christopher Agnew
    • , Pelin Ayaz
    •  & Natalia Jura

  • Article
    | Open Access

    Trans-translation, mediated by small protein B (SmpB) and transfer-messenger RNA (tmRNA), enables recycling of the ribosomes stalled on defective mRNAs in bacteria. Here, the authors report structures of the ribosome during trans-translation that reveal a translocation intermediate and elucidate the movements of the tmRNA-SmpB complex in the ribosome.

    • Charlotte Guyomar
    • , Gaetano D’Urso
    •  & Reynald Gillet

  • Article
    | Open Access

    The human Tweety homologue (TTYH) family of transmembrane proteins have been suggested to act as chloride channels. Here the authors present cryo-EM structures of the 3 human TTYH paralogs that do not display the expected features of an anion channel, and instead appear to interact with lipid-like compounds residing in the membrane; suggesting an involvement in lipid-associated processes.

    • Anastasiia Sukalskaia
    • , Monique S. Straub
    •  & Raimund Dutzler

  • Article
    | Open Access

    The SARS-CoV-2 NSP13 helicase is essential for viral replication and of interest as a drug target. Here, the authors present the crystal structures of NSP13 in the apo form and bound to either phosphate or the non-hydrolysable ATP analog AMP-PNP and discuss the helicase mechanism. They also perform a crystallographic fragment screening and identify 65 bound fragments, which could help in the design of new antiviral agents.

    • Joseph A. Newman
    • , Alice Douangamath
    •  & Opher Gileadi

  • Article
    | Open Access

    Hetero-oligomeric TRP-like channels such as PKD1L3/PKD2L1 play crucial roles in a range of physiological and pathophysiological processes. Here, the authors present the cryo-EM structures of a minimal functional murine PKD1L3/PKD2L1 complex in the absence and presence of calcium and further supported through structure-guided mutagenic studies, they discuss the mechanism of calcium-induced channel activation.

    • Qiang Su
    • , Mengying Chen
    •  & Yigong Shi

  • Article
    | Open Access

    Here, the authors present cryoEMPEM, a method for high-resolution structural analysis of vaccine-elicited polyclonal antibody responses. They apply cryoEMPEM in combination with standard serology experiments to characterize the polyclonal antibody (pAb) responses elicited in rhesus macaques by HIV Env trimer immunogens and were able to determine up to 8 different polyclonal antibody structures in complex with their respective antigen from a single cryoEM dataset.

    • Aleksandar Antanasijevic
    • , Leigh M. Sewall
    •  & Andrew B. Ward

  • Article
    | Open Access

    The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here, the authors employ an approach that uses cryo-EM single particle analysis to track the number and distribution of nucleotides bound to each subunit in the homo-oligomeric MmCpn archaeal chaperonin complex and observe that ATP binds in a statistically random manner to MmCpn both within a ring and across the rings, which shows that there is no cooperativity in ATP binding to archaeal group II chaperonins under the conditions used in this study.

    • Yanyan Zhao
    • , Michael F. Schmid
    •  & Wah Chiu

  • Article
    | Open Access

    MADS transcription factors regulate multiple aspects of plant development. Here the authors show that the intervening I domain is conserved in both type I and type II plant MADS lineages and contributes to the functional identity of the protein by influencing both DNA binding activity and dimerisation specificity.

    • Xuelei Lai
    • , Rosario Vega-Léon
    •  & Chloe Zubieta

  • Article
    | Open Access

    The cyanophage S-2L incorporates 2-aminoadenine (Z) instead of adenine into its DNA, which still pairs with thymine forming a triple hydrogen bond. Here, the authors identify a third gene mazZ located between purZ and datZ that is required for 2-aminoadenine biosynthesis and determine the crystal structures of MazZ and PurZ. They further show that co-expression of these three genes in E.coli enables 2-aminoadenine incorporation into the bacterial genome.

    • Dariusz Czernecki
    • , Frédéric Bonhomme
    •  & Marc Delarue

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