Structural biology articles within Nature Communications

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  • Article
    | Open Access

    Phosphate involvement in calcium carbonate biominerals raises questions on biomineralisation pathways. Here, the authors explore the presence of phosphate in the growing shell of the European abalone and suggest a shared mixed mineral ancestral precursor with final crystal phase being selected by mineral-associated proteins.

    • Widad Ajili
    • , Camila B. Tovani
    •  & Nadine Nassif

  • Article
    | Open Access

    As a potential zoonotic pathogen, porcine deltacoronavirus (PDCoV) has been shown to cause febrile illness in humans. Here, Ji et al. report the structures of PDCoV spike protein bound to porcine and human aminopeptidase receptors, pointing to the likely underlying mechanism of PDCoV zoonotic transmission.

    • Weiwei Ji
    • , Qi Peng
    •  & Shuijun Zhang

  • Article
    | Open Access

    Conformations sampled by a protein while it unfolds are difficult to visualize. Here, the authors develop di-ortho-phthalaldehyde cross-linkers for rapid chemical cross-linking mass spectrometry analysis and demonstrate that this method captures the conformations of protein unfolding intermediates.

    • Jian-Hua Wang
    • , Yu-Liang Tang
    •  & Xiaoguang Lei

  • Article
    | Open Access

    IP3 receptors are intracellular calcium channels involved in numerous signaling pathways. Here, the authors present the cryo-EM structures of type-3 IP3 receptors in multiple gating conformations, including the active state revealing the molecular mechanism of the receptor activation.

    • Emily A. Schmitz
    • , Hirohide Takahashi
    •  & Erkan Karakas

  • Article
    | Open Access

    Lysine benzoylation (Kbz) is a recently discovered histone modification. Here, the authors characterize writers, erasers and readers of histone Kbz in S. cerevisiae and identify non-histone proteins bearing Kbz, laying foundations to dissect the roles of Kbz in diverse cellular processes.

    • Duo Wang
    • , Fuxiang Yan
    •  & Yong Chen

  • Article
    | Open Access

    The Dbf4-dependent kinase Cdc7 (DDK) is essential for eukaryotic DNA replication. Here, the authors present a series of cryo-EM structures elucidating the versatility of this kinase in exerting an ordered phosphorylation of its essential target to promote replication initiation.

    • Jiaxuan Cheng
    • , Ningning Li
    •  & Yuanliang Zhai

  • Article
    | Open Access

    The degree to which the conformation of the human metapneumovirus fusion (F) protein affects immunogenicity has been debated. Here, Hsieh et al. engineer prefusion-stabilized F variants with enhanced thermostability that elicit higher neutralizing antibody titers in mice than postfusion F.

    • Ching-Lin Hsieh
    • , Scott A. Rush
    •  & Jason S. McLellan

  • Article
    | Open Access

    Radiation damage hampers protein structure determination by X-ray crystallography. Here, the AUs introduce the Bnet metric, a single value summarising the extent of radiation damage of a protein crystal structure, and use Bnet to detect radiation damage in structures deposited in the Protein Data Bank.

    • Kathryn L. Shelley
    •  & Elspeth F. Garman

  • Article
    | Open Access

    Ycf1, a C-family member ATP Binding Cassette (ABC) transporter, transports glutathione and glutathione-metal complexes in yeast. Here the authors use cryo-EM and biochemical analysis to show how an intrinsically-disordered regulatory domain (R-domain) controls activity upon phosphorylation by engaging with a Nucleotide Binding Domain.

    • Nitesh Kumar Khandelwal
    • , Cinthia R. Millan
    •  & Thomas M. Tomasiak

  • Article
    | Open Access

    RNA folding free energy nearest neighbor parameters were determined for sequences with the nucleotide m6A. The RNAstructure software package can accommodate modified nucleotides, enabling secondary structure prediction of sequences with m6A.

    • Elzbieta Kierzek
    • , Xiaoju Zhang
    •  & David H. Mathews

  • Article
    | Open Access

    The nonopioid sigma-1 receptor (σ1R) is localized to the endoplasmic reticulum (ER), interacts with multiple effector proteins and various synthetic ligands, and is implicated in many diseases. Here, authors provide structural and functional evidence to reveal the likely ligand entry pathway for σ1R.

    • Fuhui Meng
    • , Yang Xiao
    •  & Xiaoming Zhou

  • 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

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