Structural biology articles within Nature Communications

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  • Article
    | Open Access

    Structural and functional characterization of the full-length TRPV1 channel from the thirteen-lined ground squirrel reveal the architecture of the extracellular cap domain and the intracellular C-terminus, and suggest a role of the cap domain in TRPV1 conductance and ion selectivity.

    • Kirill D. Nadezhdin
    • , Arthur Neuberger
    •  & Alexander I. Sobolevsky

  • Article
    | Open Access

    Microbial oxidoreductases are key in biomass breakdown. Here, the authors expand the specificity and redox scope within fungal auxiliary activity 7 family (AA7) enzymes and show that AA7 oligosaccharide dehydrogenases can directly fuel cellulose degradation by lytic polysaccharide monooxygenases.

    • Majid Haddad Momeni
    • , Folmer Fredslund
    •  & Maher Abou Hachem

  • Article
    | Open Access

    Histamine receptors are effective targets for allergy treatments and antihistamines are the first choice of many allergic disorders, but the exact mechanism of agonist binding and receptor activation remain unknown. Here, the authors present the cryo-EM structure of histamine-bound H1R/Gq complex and propose a mechanism of ligand induced receptor activation.

    • Ruixue Xia
    • , Na Wang
    •  & Yuanzheng He

  • Article
    | Open Access

    Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn3+SOD and Mn2+SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.

    • Jahaun Azadmanesh
    • , William E. Lutz
    •  & Gloria E. O. Borgstahl

  • Article
    | Open Access

    How DNA polymerases discriminate against oxidized and undamaged nucleotides during DNA repair is not fully understood. Here, the authors reveal high-resolution timelapse X-ray crystallography snapshots of DSB repair polymerase μ undergoing DNA synthesis providing mechanistic insights into the process.

    • Joonas A. Jamsen
    • , Akira Sassa
    •  & Samuel H. Wilson

  • Article
    | Open Access

    The Drosophila tumour necrosis factor (TNF) system comprises a single ligand Eiger (Egr) and two receptors. The structure of Egr in complex with the extracellular domain of the receptor Grindelwald and accompanying data suggest that distinct affinities of TNF ligand for its receptors mediate non-redundant functions.

    • Valentina Palmerini
    • , Silvia Monzani
    •  & Marina Mapelli

  • Article
    | Open Access

    Cytosolic coat proteins capture secretory cargo and sculpt membrane carriers for intracellular transport, such as COPII which mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Here authors visualise the complete, membrane-assembled COPII coat by cryo-electron tomography and subtomogram averaging, revealing the full network of interactions within and between coat layers.

    • Joshua Hutchings
    • , Viktoriya G. Stancheva
    •  & Giulia Zanetti

  • Article
    | Open Access

    The essential SARS-CoV-2 3CL protease is of interest as a drug target. Here, the authors identify three 3CL inhibitors and characterize them both in vitro and with a cell-based assay, and they also present the inhibitor-bound 3CL crystal structures, which may allow for the design of improved compounds.

    • Sho Iketani
    • , Farhad Forouhar
    •  & David D. Ho

  • Article
    | Open Access

    The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.

    • Christopher R. Horne
    • , Hariprasad Venugopal
    •  & Renwick C. J. Dobson

  • Article
    | Open Access

    Tomographic reconstructions of cryopreserved specimens enable in-situ structural studies. Here, the authors present the beam image-shift electron cryo-tomography (BISECT) approach that accelerates data collection speed and improves the map resolution compared to earlier approaches and present the in vitro structure of a 300 kDa protein complex that was solved at 3.6 Å resolution as a test case.

    • Jonathan Bouvette
    • , Hsuan-Fu Liu
    •  & Alberto Bartesaghi

  • Article
    | Open Access

    Conformational changes of HIV’s Env protein are required for its function in fusing the viral and host cell membranes. Here the authors describe how two small molecules alter the confirmation of Env trimers, and show they can induce structural changes similar to those occur upon receptor binding.

    • Claudia A. Jette
    • , Christopher O. Barnes
    •  & Pamela J. Bjorkman

  • Article
    | Open Access

    Buried charged networks in proteins are often important for their biological functionality and are believed to destabilise the protein fold. Here, the authors combine computational design, MD simulations, biophysical experiments, NMR and X-ray crystallography to design and characterise artificial 4α-helical proteins with buried charged elements. They analyse their conformational landscapes and observe that the ion-pairs are stabilised by amphiphilic residues that electrostatically shield the charged motif, which increases structural stability.

    • Mona Baumgart
    • , Michael Röpke
    •  & Ville R. I. Kaila

  • Article
    | Open Access

    Cryptophytes acquired plastids from red algae but replaced the light-harvesting phycobilisome with a unique cryptophyte antenna. Here via analysis of phycobilisome cryo-EM structures, Rathbone et al. propose that the α subunit of the cryptophyte antenna originated from phycobilisome linker proteins

    • Harry W. Rathbone
    • , Katharine A. Michie
    •  & Paul M. G. Curmi

  • Article
    | Open Access

    Plasmodium falciparum moves by an atypical process called gliding motility which comprises of atypical myosin A (PfMyoA) and filaments of the dynamic and divergent PfActin-1 (PfAct1). Here authors present the cryo-EM structure of PfMyoA bound to filamentous PfAct1 stabilized with jasplakinolide and provide insights into the interactions that are required for the parasite to produce the force and motion required for infectivity.

    • Julien Robert-Paganin
    • , Xiao-Ping Xu
    •  & Dorit Hanein

  • Article
    | Open Access

    Biogenesis of small nucleolar RNAs ribonucleoproteins (snoRNPs) requires dedicated assembly machinery. Here, the authors show that a subset of snoRNP assembly factors interacts, genetically or directly, with factors modulating chromatin architecture, suggesting a link between ribosome formation and chromatin functions.

    • Benoît Bragantini
    • , Christophe Charron
    •  & Bruno Charpentier

  • Article
    | Open Access

    Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.

    • Saminathan Ramakrishnan
    • , Jason R. Stagno
    •  & Yun-Xing Wang

  • Article
    | Open Access

    Erythromycin esterases (Eres) cleave the macrolactone ring of macrolides, a class of widely used antibiotics. Structures of EreC, in silico flexible docking studies and previous mutagenesis data lead to the proposal of a detailed catalytic mechanism for the Ere family of enzymes.

    • Michał Zieliński
    • , Jaeok Park
    •  & Albert M. Berghuis

  • Article
    | Open Access

    Chromosome segregation requires the association of the kinetochore protein complex with a specialized nucleosome at the centromere. Here, the authors present cryo-EM and mutational studies that provide insights into the structure of the budding yeast centromeric nucleosome and how the centromere CBF3 protein complex guides its formation.

    • Ruifang Guan
    • , Tengfei Lian
    •  & Yawen Bai

  • Article
    | Open Access

    Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C4, an intracrine mediator of cell death. Structural, biochemical and computational analyses of human MGST2 suggest a mechanism employed by the enzyme to restrict catalysis to only one active site within the MGST2 trimer.

    • Madhuranayaki Thulasingam
    • , Laura Orellana
    •  & Jesper Z. Haeggström

  • Article
    | Open Access

    Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Here authors report the cryo-EM structure of bafilomycin A1-bound V-ATPase with six bafilomycin A1 molecules bound to the c-ring and reveal the molecular basis for Bafilomycin A1 inhibition of the V-ATPase.

    • Rong Wang
    • , Jin Wang
    •  & Xiaochun Li

  • Article
    | Open Access

    Antibiotic-resistant bacterial pathogens pose a substantial threat to human health. Here, aided by structural analyses, the authors describe the molecular mechanism behind the activity of a series of compounds that inhibit trans-translation and are effective in eradicating N. gonorrhoeae infection in mice.

    • Zachary D. Aron
    • , Atousa Mehrani
    •  & Kenneth C. Keiler

  • Article
    | Open Access

    Influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion activities. Here, the authors apply electron cryotomography of whole virus together with subtomogram averaging to determine the HEF structure and lattice organisation on the viral membrane and they discuss mechanistic implications for virus budding and membrane fusion.

    • Steinar Halldorsson
    • , Kasim Sader
    •  & Peter B. Rosenthal

  • Article
    | Open Access

    X-ray fee-electron lasers (XFELs) enable time-resolved crystallography experiments and the structure determination of proteins with little or no radiation damage. However currently it is unknown whether the designated 4.5 MHz maximum pulse rate for the European XFEL could lead to sample damage caused by shock waves from preceding pulses. Here, the authors address this question by performing a X-ray pump X-ray probe experiment on haemoglobin microcrystals at the Stanford XFEL facility that mimics the 4.5 MHz data collection mode and observe structural changes and a drop in diffraction data quality of the crystals.

    • Marie Luise Grünbein
    • , Alexander Gorel
    •  & Ilme Schlichting

  • Article
    | Open Access

    14-3-3 proteins recognize phosphorylated motifs within numerous protein partners. Here, the authors characterize the binding of all human 14-3-3 isoforms to four E6 oncoproteins, and identify a fixed order of 14-3-3 binding affinities that is conserved in 14-3-3:phosphoprotein interactions across the proteome.

    • Gergo Gogl
    • , Kristina V. Tugaeva
    •  & Nikolai N. Sluchanko

  • Article
    | Open Access

    Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) patients have brain deposits with amyloid-like aggregates from large C-terminal fragments of the transactive response DNA-binding protein of 43 kDa (TDP-43). Here, the authors present the cryo-EM structure of amyloid fibrils generated from the complete C-terminal TDP-43 low complexity domain and they discuss the effects of disease-causing mutations and phosphorylation of specific Ser residues.

    • Qiuye Li
    • , W. Michael Babinchak
    •  & Witold K. Surewicz

  • Article
    | Open Access

    Previous work identified goddard as a putative de novo evolved gene in Drosophila melanogaster. Here, the authors characterize the structure and function of the Goddard protein in D. melanogaster, and they infer its ancestral and extant structures across the Drosophila genus.

    • Andreas Lange
    • , Prajal H. Patel
    •  & Erich Bornberg-Bauer

  • Article
    | Open Access

    Some bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, Strømland et al. identify NADases on the surface of fungal spores, and show that the enzymes display unique biochemical and structural properties.

    • Øyvind Strømland
    • , Juha P. Kallio
    •  & Mathias Ziegler

  • Article
    | Open Access

    The SRC Homology 3 (SH3) domains mediate protein–protein interactions (PPIs). Here, the authors assess the SH3-mediated PPIs in yeast, and show that the identity of the protein itself and the position of the SH3 both affect the interaction specificity and thus the PPI-dependent cellular functions.

    • Ugo Dionne
    • , Émilie Bourgault
    •  & Christian R. Landry

  • Article
    | Open Access

    Reveromycin A (RM-A) selectively inhibits eukaryotic cytoplasmic isoleucyltRNA synthetase (IleRS). Herein, the authors show that RM-A molecule occupies the tRNAIle binding site of Saccharomyces cerevisiae IleRS, and that RM-A cooperates with isoleucine or isoleucyl-adenylate for IleRS binding.

    • Bingyi Chen
    • , Siting Luo
    •  & Huihao Zhou

  • Article
    | Open Access

    The spike glycoprotein in coronaviruses is a key viral protein for cross-species transmission and infection. Here, the authors present the cryo-EM structures of the spike ectodomains from bat and pangolin coronaviruses, compare them with the available SARS-CoV-2 spike structures and discuss implications for the evolution and cross-species transmission of SARS-CoV-2.

    • Shuyuan Zhang
    • , Shuyuan Qiao
    •  & Xinquan Wang

  • Article
    | Open Access

    Cooperation between the ULK complex and autophagy receptors mediates targeting cargoes to autophagosomes. Here, the authors show that interactions of ULK subunit FIP200 with autophagy receptors CCPG1 and Optineurin can be regulated by phosphorylation, suggesting a general binding mode shared by autophagy receptors.

    • Zixuan Zhou
    • , Jianping Liu
    •  & Lifeng Pan

  • Article
    | Open Access

    The phosphatidylinositol-3-phosphate (PI3P) is generated by the lipid kinase VPS34, in the context of VPS34 complex I on autophagosomes or complex II on endosomes. Biochemical and structural analyses provide insights into the mechanism of both VPS34 complexes recruitment to and activation on membranes by specific Rab GTPases.

    • Shirley Tremel
    • , Yohei Ohashi
    •  & Roger L. Williams

  • Article
    | Open Access

    Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) is important for invasion of reticulocytes and PvRBP2b antibodies correlate with protection. Here, Chan et al. isolate and characterize anti-PvRBP2b human monoclonal antibodies and describe mechanisms by which these antibodies inhibit invasion.

    • Li-Jin Chan
    • , Anugraha Gandhirajan
    •  & Wai-Hong Tham

  • Article
    | Open Access

    So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.

    • William M. Dawson
    • , Eric J. M. Lang
    •  & Derek N. Woolfson

  • Article
    | Open Access

    Virulent type III secretion systems (T3SSs) or injectisomes enable pathogenic bacteria to inject effector proteins directly into the host cell cytoplasm. Structures of a needle complex engaged with the effector protein reveal the complete secretion channel and provide insights into the mechanism of substrate translocation through T3SSs.

    • Sean Miletic
    • , Dirk Fahrenkamp
    •  & Thomas C. Marlovits

  • Article
    | Open Access

    ATP-dependent helicases remodel the spliceosome and proofread splice site recognition. A new method – Purified Spliceosome iCLIP (psiCLIP) – probes protein-RNA interactions in defined spliceosome complexes to reveal how the helicases Prp16 and Prp22 promote correct mRNA synthesis through dynamic binding on their RNA substrates.

    • Lisa M. Strittmatter
    • , Charlotte Capitanchik
    •  & Kiyoshi Nagai

  • Article
    | Open Access

    The lipid regulation of mammalian ion channel function has emerged as a fundamental mechanism in the control of electrical signalling and transport specificity. Here, the authors combine molecular dynamics simulations, mutagenesis, and electrophysiology to provide mechanistic insights into how lipophilic molecules alter gating kinetics and K+ currents of hERG1.

    • Williams E. Miranda
    • , Jiqing Guo
    •  & Sergei Yu. Noskov

  • Article
    | Open Access

    Our understanding of the residue-level details of protein interactions remains incomplete. Here, the authors show sequence coevolution can be used to infer interacting proteins with residue-level details, including predicting 467 interactions de novo in the Escherichia coli cell envelope proteome.

    • Anna G. Green
    • , Hadeer Elhabashy
    •  & Debora S. Marks

  • Article
    | Open Access

    Glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR) and GITR ligand (GITRL) regulate immune cell activities, including anti-tumor immune responses. Structures and visualization of human and mouse GITR–GITRL complexes offer insight into the architecture of higher-order membrane assemblies, and their signaling.

    • Feng Wang
    • , Bryant Chau
    •  & Pavel Strop

  • Article
    | Open Access

    2,5-Dihydroxypyridine dioxygenase NicX uses a mononuclear non-heme Fe(II) to catalyze the oxidative pyridine ring cleavage of the pollutant 2,5-hydroxypyridine. Here, the authors report crystal structures of NicX, identify residues involved in substrate stabilization and Fe(II) coordination, and propose the catalytic mechanism of NicX.

    • Gongquan Liu
    • , Yi-Lei Zhao
    •  & Ping Xu

  • Article
    | Open Access

    Here, the authors present two local methods for analyzing cryo-EM maps: LocSpiral and LocBSharpen that enhance high-resolution features of cryoEM maps, while preventing map distortions. They also introduce LocBFactor and LocOccupancy, which allow obtaining local B-factors and electron density occupancy maps from cryo-EM reconstructions and the authors demonstrate that these methods improve the interpretability and analysis of cryo-EM maps using different test cases among them recent SARS-CoV-2 spike glycoprotein structures.

    • Satinder Kaur
    • , Josue Gomez-Blanco
    •  & Javier Vargas

  • Article
    | Open Access

    Bacterial malic enzymes (ME) transform malate to pyruvate. One group, hybrid ME enzymes, are regulated by acetyl-CoA, linking the enzyme activity to the metabolic state of the cell. Structures of a representative hybrid ME MaeB reveal large conformational rearrangements that provide insight into the mechanism of allosteric inhibition by acetyl-CoA.

    • Christopher John Harding
    • , Ian Thomas Cadby
    •  & Andrew Lee Lovering

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