Structural biology articles within Nature Communications

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  • Article
    | Open Access

    Predicting the structure of protein complexes is extremely difficult. Here, authors apply AlphaFold2 with optimized multiple sequence alignments to model complexes of interacting proteins, enabling prediction of both if and how proteins interact with state-of-art accuracy.

    • Patrick Bryant
    • , Gabriele Pozzati
    •  & Arne Elofsson

  • Article
    | Open Access

    The proteasome complexes, composed of 20S core particles and one or two regulatory particles (proteasome activators), degrade most eukaryotic proteins. Here, the authors identify a sequence motif and resolve its interactions mediating the activation of the human 20S proteasome.

    • Kwadwo A. Opoku-Nsiah
    • , Andres H. de la Pena
    •  & Jason E. Gestwicki

  • Article
    | Open Access

    The rotary ATPases use a rotary catalytic mechanism to drive transmembrane proton movement powered by ATP hydrolysis. Here, the authors report a collection of V/A-ATPase V1 domain structures, providing insights into rotary mechanism of the enzyme and potentially other rotary motor proteins driven by ATP hydrolysis.

    • J. Kishikawa
    • , A. Nakanishi
    •  & K. Yokoyama

  • Article
    | Open Access

    Nuclear translocation of the p50/p65 heterodimer is essential for NF-κB signaling. Here, the authors identify a bipartite Nuclear Localization Signal in the NF-κB p50/p65 heterodimer that is recognized with high affinity by importin α3.

    • Tyler J. Florio
    • , Ravi K. Lokareddy
    •  & Gino Cingolani

  • Article
    | Open Access

    The SARS-CoV-2 spike has been evolving in the human population. The variants of concern alpha and beta evolved to optimise spike openness and so ability to bind its receptor ACE2, the affinity towards the receptor, and stability upon receptor binding.

    • Antoni G. Wrobel
    • , Donald J. Benton
    •  & Steven J. Gamblin

  • Article
    | Open Access

    Many bacteria can take up exogenous DNA, in a process that often requires surface appendages composed of thousands of protein subunits called pilins. Here, Braus et al. show that a minor pilin binds directly to DNA and is important for DNA uptake in the pathogen Legionella pneumophila.

    • Sebastian A. G. Braus
    • , Francesca L. Short
    •  & Manuela K. Hospenthal

  • Article
    | Open Access

    Attachment of ubiquitin to proteins is tightly regulated and controls many signalling pathways. Here, the authors show that addition of ubiquitin by the RING E3 ligases Arkadia and Ark2C is enhanced by ubiquitin and a charged loop that precedes the RING domain.

    • Andrej Paluda
    • , Adam J. Middleton
    •  & Catherine L. Day

  • Article
    | Open Access

    This study determined the structure of the spike protein of the SARS-CoV-2 omicron variant, revealing a predominantly open conformation of the molecule that may help omicron infect cells more efficiently than do previous variants.

    • Gang Ye
    • , Bin Liu
    •  & Fang Li

  • Article
    | Open Access

    In the paper, Dr. Wang et al reported a cryo-EM structure of the human leukotriene B4 receptor 1 (BLT1) in complex with its native ligand leukotriene B4 (LTB4) in an active conformation complexed with Gi protein. The structure reveals the molecule determinant of LTB4 binding and the mechanism of receptor activation. These structural information will boost the understanding of LTB4-BLT1 signaling and provide a rational basis for designing novel anti-leukotriene drugs.

    • Na Wang
    • , Xinheng He
    •  & Yuanzheng He

  • Article
    | Open Access

    EndoE is a multi-domain glycoside hydrolase of the human pathogen Enterococcus faecalis. Here, the authors present crystal structures of EndoE and provide biochemical insights into the molecular basis of EndoE’s substrate specificity and catalytic mechanism.

    • Mikel García-Alija
    • , Jonathan J. Du
    •  & Marcelo E. Guerin

  • Article
    | Open Access

    The S-layer is a two-dimensional protein array that covers the cell surface of many bacteria and archaea. Here, the authors use high-resolution X-ray crystallography and electron microscopy to provide detailed insights into S-layer organisation and assembly for the bacterial pathogen Clostridioides difficile.

    • Paola Lanzoni-Mangutchi
    • , Oishik Banerji
    •  & Paula S. Salgado

  • Article
    | Open Access

    G-wire structures have potential applications in bio-nanotechnology, however, this is limited by a lack of understanding about the assembly process and structures formed. Here, the authors use nuclear magnetic resonance and molecular dynamic simulations to understand the guiding principles of G-wire assembly.

    • Daša Pavc
    • , Nerea Sebastian
    •  & Primož Šket

  • Article
    | Open Access

    Bacterial responses to nutrient limitation and other stress conditions are often modulated by the nucleotide-based second messenger (p)ppGpp. Here, the authors show that (p)ppGpp inhibits the SRP membrane-protein insertion and secretion pathway by binding to GTPases Ffh and FtsY.

    • Laura Czech
    • , Christopher-Nils Mais
    •  & Gert Bange

  • Article
    | Open Access

    Adenylyl cyclases (ACs) generate the second messenger cAMP and play an important role in cellular signaling. Here, the authors use cryo-EM to trace the conformational changes resulting from binding to partial and full activators to one of these enzymes, AC9.

    • Chao Qi
    • , Pia Lavriha
    •  & Volodymyr M. Korkhov

  • Article
    | Open Access

    LtaA catalyzes glycolipid translocation by a ‘trap-and-flip’ mechanism, pointing to a shared mechanistic model among MFS lipid transporters. Asymmetric lateral openings allow access of the entire lipid substrate to the amphipathic central cavity.

    • Elisabeth Lambert
    • , Ahmad Reza Mehdipour
    •  & Camilo Perez

  • Article
    | Open Access

    Selective targeting individual subtypes of N-methyl-D-aspartate receptors (NMDARs) is a desirable therapeutic strategy for neurological disorders. Here, the authors report identification of a functional antibody that specifically targets and allosterically down-regulates ion channel activity of the GluN1—GluN2B NMDAR subtype.

    • Nami Tajima
    • , Noriko Simorowski
    •  & Hiro Furukawa

  • Article
    | Open Access

    Rebelo-Guiomar et al. unveil late stage assembly intermediates of the human mitochondrial ribosome by inactivating the methyltransferase MRM2 in cells. Absence of MRM2 impairs organismal homeostasis, while its catalytic activity is dispensable for mitoribosomal biogenesis.

    • Pedro Rebelo-Guiomar
    • , Simone Pellegrino
    •  & Michal Minczuk

  • Article
    | Open Access

    HAESA and HSL2 are receptors for IDA/IDL-family signaling peptides in plants. Here the authors show that HSL1, previously shown to recognize CLE9, preferentially binds IDA/IDL peptides and regulates leaf epidermal patterning independently of CLE peptides.

    • Andra-Octavia Roman
    • , Pedro Jimenez-Sandoval
    •  & Julia Santiago

  • Article
    | Open Access

    The human neuropeptide Y (NPY) acts through G-protein coupled receptors and is involved in food intake, stress response, anxiety, and memory retention. Here, the authors show that, unlike in other neuropeptides, both the N-terminal and the C-terminal regions of NPY interact with the NPY receptor 1.

    • Chaehee Park
    • , Jinuk Kim
    •  & Hee-Jung Choi

  • Article
    | Open Access

    The interplay of the proteasome and deubiquitinase Ubp6 is crucial for the degradation of ubiquitylated substrates. Here, the authors provide structural insights into the allosteric mechanism by which the activities of both Ubp6 and the proteasome are regulated.

    • Ka Ying Sharon Hung
    • , Sven Klumpe
    •  & Daniel Finley

  • Article
    | Open Access

    The intracellular domain (ICD) of Cys-loop receptors mediates many of their functions, but no complete structure of a Cys-loop receptor ICD is available to date. Here, the authors combine NMR and ESR spectroscopy to determine the full-length ICD structures of the human α7 nicotinic acetylcholine receptor (α7nAChR).

    • Vasyl Bondarenko
    • , Marta M. Wells
    •  & Pei Tang

  • Article
    | Open Access

    Molecular glue has been used as a broad term describing a class of protein interaction-promoting compounds. Here, the authors outline two unifying thermodynamic features to formally define molecular glues and guide their prospective discovery.

    • Shiyun Cao
    • , Shoukai Kang
    •  & Ning Zheng

  • Article
    | Open Access

    AMPA glutamate receptors, mediate the majority of excitatory signaling in the brain. Here the authors show how the auxiliary subunit TARP-γ8 shapes gating kinetics, ion conductance and rectification properties of the heteromeric GluA1/2 AMPA receptor.

    • Beatriz Herguedas
    • , Bianka K. Kohegyi
    •  & Ingo H. Greger

  • Article
    | Open Access

    Liu et al. report structures of human sphingosine 1-phosphate (S1P) receptor 1 (S1P1) in complex with Gi and S1P or the multiple sclerosis (MS) drug Siponimod, as well as human lysophosphatidic acid (LPA) receptor 1 (LPA1) in complex with Gi and LPA, revealing distinct conformations of the lysophospholipids interacting with their cognate GPCRs.

    • Shian Liu
    • , Navid Paknejad
    •  & Xin-Yun Huang

  • Article
    | Open Access

    Neutralizing antibodies (bNAbs) against HIV-1 are exclusively directed against the viral envelope protein (Env) and mainly target Env in a closed, prefusion state. Here, Yang et al. structurally characterize two heterologously-neutralizing CD4-binding site (CD4bs) antibodies isolated from sequentially immunized macaques, and show that these antibodies recognize the CD4bs on Env trimers in an „occluded-open‟ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4.

    • Zhi Yang
    • , Kim-Marie A. Dam
    •  & Pamela J. Bjorkman

  • Article
    | Open Access

    Tousled-like kinase 2 (TLK2) phosphorylates ASF1 histone chaperones to promote nucleosome assembly in S phase. Here, the authors show that TLK2 targets ASF1 by simulating its client protein histone H3, exploiting a primordial protein interaction surface for regulatory control.

    • Bertrand Simon
    • , Hua Jane Lou
    •  & David A. Calderwood

  • Article
    | Open Access

    Type 2 bradykinin receptor (B2R) is essential in vasodilation and cardioprotection. Here the authors present two cryo-EM structures of human B2R-Gq in complex with bradykinin and kallidin to elucidate the mechanisms for ligand binding, receptor activation, and Gq proteins coupling.

    • Jinkang Shen
    • , Dongqi Zhang
    •  & Haitao Zhang

  • Article
    | Open Access

    The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.

    • Lavinia Gambelli
    • , Michail N. Isupov
    •  & Bertram Daum

  • Article
    | Open Access

    HIV envelope is a target for vaccine development, but induction of broadly neutralizing antibodies has been difficult. Here, the authors show that electroporation with a synthetic DNA vaccine construct allows in vivo production of HIV envelope native like trimers to induce autologous tier-2 neutralizing antibodies targeting a C3/V5 epitope in mice.

    • Ziyang Xu
    • , Susanne Walker
    •  & Daniel W. Kulp

  • Article
    | Open Access

     The Arp2/3 complex inhibitor Arpin controls cell migration by interrupting a feedback loop involving Rac-WAVE-Arp2/3 complex Here, the authors use structural, biochemical, and cellular studies to reveal Arpin’s mechanism of inhibition.

    • Fred E. Fregoso
    • , Trevor van Eeuwen
    •  & Roberto Dominguez

  • Article
    | Open Access

    The drug AT-527 targets the SARS-CoV-2 replication machinery. Here the authors use Cryo-EM to show how AT-527 inhibits SARS-CoV-2 polymerase by acting as an immediate RNA chain terminator and stably binding in a NiRAN active-site pocket; impeding an essential nucleotide-transfer activity.

    • Ashleigh Shannon
    • , Véronique Fattorini
    •  & Bruno Canard

  • Article
    | Open Access

    The cell wall of the bacterial pathogen Group A Streptococcus is decorated with a polysaccharide termed GAC, which is a target for vaccine development. Here, Rush et al. characterize the linkage between GAC and peptidoglycan, and identify a protein that deacetylates the linkage and thus protects the pathogen against host cationic antimicrobial proteins.

    • Jeffrey S. Rush
    • , Prakash Parajuli
    •  & Natalia Korotkova

  • Article
    | Open Access

    Many parasitic organisms contain molecular structures that are drastically smaller than analogous structures in non-parasitic organisms. Here the authors describe a cryo-EM structure of the ribosome from E. cuniculi that reveals that it compensated rRNA truncations by evolving the ability to use small molecules as ribosomal building blocks.

    • David Nicholson
    • , Marco Salamina
    •  & Sergey V. Melnikov

  • Article
    | Open Access

    The catalytic domains in nonribosomal peptide synthetases (NRPSs) are responsible for a choreography of events that elongates substrates into natural products. Here, the authors present cryo-EM structures of a siderophore-producing dimeric NRPS elongation module in multiple distinct conformations, which provides insight into the mechanisms of catalytic trajectory.

    • Jialiang Wang
    • , Dandan Li
    •  & Zhijun Wang

  • Article
    | Open Access

    Five New World mammarenaviruses (NWMs) enter cells via binding to human transferrin receptor 1 (hTfR1). Here, Hickerson et al. show that hTfR1 targeting antibodies partially protect hTfR1-transgenic mice from lethal NWM challenge via competition of anti-hTfR1 antibody and viral glycoprotein for hTfR1.

    • Brady T. Hickerson
    • , Tracy R. Daniels-Wells
    •  & Brian B. Gowen

  • Article
    | Open Access

    Nonribosomal peptide synthetases work with additional enzymes to synthesise secondary metabolites and therapeutics. Here, the authors explore bacillamide D synthesis and show the oxidase action is done while the intermediate is attached to the synthetase and replicate this with an oxidase bound synthetase for bioengineering applications.

    • Camille Marie Fortinez
    • , Kristjan Bloudoff
    •  & T. Martin Schmeing

  • Article
    | Open Access

    Zhang and Cui et al. present in situ cryoEM structures of the trimeric spike of cytoplasmic polyhedrosis virus in both open and close conformations, and demonstrate that spike detachment from the capsid is triggered by the presence of SAM and ATP.

    • Yinong Zhang
    • , Yanxiang Cui
    •  & Z. Hong Zhou

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