Structural biology articles within Nature Communications

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  • Article
    | Open Access

    ThiH is a radical SAM L-tyrosine lyase involved in the biosynthesis of the thiazole ring of vitamin B1. Here, the authors report the crystal structure of ThiH in complex with its L-tyrosine substrate, revealing an unexpected protonation state and tunneling effect that lowers the reaction energy barrier.

    • Patricia Amara
    • , Claire Saragaglia
    •  & Yvain Nicolet

  • Article
    | Open Access

    CryoEM of mitochondrial ATP synthase frozen during rotary catalysis reveals dramatic conformational changes in the peripheral stalk subcomplex, which enable the enzyme’s efficient synthesis of ATP.

    • Hui Guo
    •  & John L. Rubinstein

  • Article
    | Open Access

    Despite their relevance as regulators of actin severing and filament disassembly, few structural insights into the mechanism of cofilin-isoform-specific severing activity are reported. Here, the authors provide structural insights towards actin severing activity by human cofilin-2 obtained by MAS NMR and all-atom MD simulations. The results reveal an isoform-specific binding mode unique to CFL2 that may be related to its potent severing properties in-vivo.

    • Jodi Kraus
    • , Ryan W. Russell
    •  & Tatyana Polenova

  • Article
    | Open Access

    T-type calcium channels are implicated in many diseases. Here, multiple structures of CaV3.3 channel elucidate molecular mechanisms of T-type CaV channels activation at low voltage and interaction with different clinically used channel blockers.

    • Lingli He
    • , Zhuoya Yu
    •  & Yan Zhao

  • Article
    | Open Access

    Bacterial photosynthesis reflects the early stages of the evolution of photosynthesis. Here, the authors present a systematic study of the cryo-EM structures of the dimeric light harvesting–reaction center complexes and assembly variants from Rhodobacter sphaeroides, which delineated a hierarchical assembly pathway and quinone transport routes of the dimeric photosynthetic RC–LH1 core complex.

    • Peng Cao
    • , Laura Bracun
    •  & Lu-Ning Liu

  • Article
    | Open Access

    Complement activation on foreign cell surfaces leads to the generation of complement opsonins, which activate complement receptor type 3 (CR3) and pathogen clearance by macrophages. Here, the authors reveal structural basis of the interaction between human opsonin iC3b and the von Willebrand A inserted domain of the α chain of CR3.

    • Francisco J. Fernández
    • , Jorge Santos-López
    •  & M. Cristina Vega

  • Article
    | Open Access

    Phages use anti-CRISPR proteins (Acrs) to counteract the bacterial CRISPR-Cas systems. Here, the authors characterize AcrIF24, which functions as an Aca (Acr-associated) to repress and regulate its own transcription, dimerizes the Csy complex, blocks the hybridization of target DNA, and tethers non-sequence-specific DNA to the Csy complex.

    • Lingguang Yang
    • , Laixing Zhang
    •  & Yue Feng

  • Article
    | Open Access

    Rhodobacter sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present structures of its native dimeric and a protein-U-lacking monomeric light-harvesting-reaction center complexes, which reveal asymmetric features for the dimer and an altered shape for the monomer.

    • Kazutoshi Tani
    • , Ryo Kanno
    •  & Zheng-Yu Wang-Otomo

  • Article
    | Open Access

    Here the authors describe the Waffle Method, aimed at increasing the throughput of and solves several challenges present in cryo-FIB/SEM sample preparation for cryo-ET analysis — the highest-resolution method for obtaining 3D views of native biological specimens in-situ.

    • Kotaro Kelley
    • , Ashleigh M. Raczkowski
    •  & Alex J. Noble

  • Article
    | Open Access

    The essential protein kinase PDK1 is activated by phospoinositide-mediated dimerization and trans-autophosphorylation. Here, the authors show that in the absence of PIP3 or PI(3,4)P2 phosphoinositides, PDK1 is maintained in an inactive, autoinhibited conformation in the cytosol.

    • Aleksandra Levina
    • , Kaelin D. Fleming
    •  & Thomas A. Leonard

  • Article
    | Open Access

    Presequence protease (PreP) is essential to mitochondrial proteostasis. This study leverages advanced vitrification techniques to solve cryoEM structures of apo- and substrate-bound PreP and integrates these data with other analysis to reveal key stages and mechanistic insights of the PreP catalytic cycle.

    • Wenguang G. Liang
    • , Juwina Wijaya
    •  & Wei-Jen Tang

  • Article
    | Open Access

    Influenza virus neuraminidase (NA) is a drug target and a potential vaccine antigen. Here, the authors provide a detailed analysis of the conformational stability of NA, and show how expression and stability of recombinant NA antigens can be strengthened through structure-based design.

    • Daniel Ellis
    • , Julia Lederhofer
    •  & Masaru Kanekiyo

  • Article
    | Open Access

    Direct information on the dynamic interplay between membrane proteins and lipids is scarce. Here the authors report a detailed description of these close relationships by combining lipid nanodiscs and high-pressure NMR. They report the link between pressure and lipid compositions to the conformational landscape of the β-barrel OmpX and the α-helical BLT2 G Protein-Coupled Receptor in nanodiscs.

    • Alexandre Pozza
    • , François Giraud
    •  & Laurent J. Catoire

  • Article
    | Open Access

    The formyl peptide receptor 2 (FPR2) is involved in the pathogenesis of Alzheimer’s disease. Structures of FPR2 bound to Aβ42, humanin, or formyl peptides offer insight into Aβ42 neurotoxicity, humanin neuroprotection, and FPR ligand selectivity

    • Ya Zhu
    • , Xiaowen Lin
    •  & Beili Wu

  • Article
    | Open Access

    Immature poxviruses are characterized by nonicosahedral semiordered protein scaffolds critical for morphogenesis. Here, the authors use cryo-EM structures of Vaccinia virus D13 scaffold intermediates to explain their assembly mechanism.

    • Jaekyung Hyun
    • , Hideyuki Matsunami
    •  & Matthias Wolf

  • Article
    | Open Access

    The structural basis for urokinase-type plasminogen activator receptor (uPAR) dimerization is not understood. Here, the authors solve the crystal structure of soluble uPAR dimers, identifying substantial structural changes compared to the monomer.

    • Shujuan Yu
    • , Yaqun Sui
    •  & Mingdong Huang

  • Article
    | Open Access

    The S9.6 monoclonal antibody is widely used to map R-loops genome wide. Here, Bou-Nader et al., define the nucleic acid-binding specificity of S9.6 and report its crystal structures free and bound to a hybrid, which reveal the asymmetric recognition of the RNA and DNA strands and its A-form conformation.

    • Charles Bou-Nader
    • , Ankur Bothra
    •  & Jinwei Zhang

  • Article
    | Open Access

    MERS-CoV ORF4b antagonizes host innate immune response, partially via blocking nuclear import adapter IMPα activity and preventing nuclear translocation of NF-κB. Here, Munasinghe and Edwards et al. biochemically and structurally define the interaction between ORF4b and IMPα-family members and find a non-canonical interaction between ORF4b NLS and IMPα2 and IMPα3.

    • Thilini S. Munasinghe
    • , Megan R. Edwards
    •  & Jade K. Forwood

  • Article
    | Open Access

    Constriction of the selectivity filter is assumed to be a hallmark of C-type inactivation in K+ channels. Using different high-resolution methods, this study shows a distinct C-type inactivation mechanism in a KcsA mutant that emulates Kv-channels.

    • Ahmed Rohaim
    • , Bram J. A. Vermeulen
    •  & Markus Weingarth

  • Article
    | Open Access

    Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases responsible for significant economic losses in the swine industry. The authors report the structures of the PRV A-capsid and C-capsid, shedding light on PRV’s assembly mechanism.

    • Guosong Wang
    • , Zhenghui Zha
    •  & Ningshao Xia

  • Article
    | Open Access

    Pausing of RNA polymerase (RNAP) and transcription is regulated by the NusA and NusG transcription factors in bacteria. Here the authors provide structural evidence for how they interact with RNAP to carry out their pausing roles and also reveal functions for NusA and NusG in transcription termination.

    • Chengjin Zhu
    • , Xieyang Guo
    •  & Albert Weixlbaumer

  • Article
    | Open Access

    RNA molecules exhibit conformational fluctuations between ground states and excited states. Here the authors designed and verified small hairpin RNAs with predefined secondary structure reshufflings. In light of Van’t Hoff analysis and accelerated molecular dynamics simulation, a mechanism of multistep sequential transition has been revealed.

    • Ge Han
    •  & Yi Xue

  • 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

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