Structural biology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    The mechanism by which RING E3-anchored ubiquitin chains are formed is not well understood. Here, the authors solve a crystal structure of the RING E3 enzyme TRIM21 trapped in the process of self-anchored chain elongation and provide biochemical and cellular insights into the mechanism of ubiquitin conjugation.

    • Leo Kiss
    • , Dean Clift
    •  & Leo C. James

  • Article
    | Open Access

    The molecular details of the RAS-RAF interaction are still not fully understood. Here, the authors present crystal structures of wild-type and mutant KRAS in complex with the RAS-binding and membrane-interacting cysteine-rich domains of RAF1, and propose a model of the membrane-bound RAS-RAF complex.

    • Timothy H. Tran
    • , Albert H. Chan
    •  & Dhirendra K. Simanshu

  • Article
    | Open Access

    Transcription activation of late genes in T4 bacteriophage requires the promoter specificity factor gp55, the coactivator gp33 and the sliding clamp gp45. Here, the authors provide structural insights into gp45- dependent transcription activation by determining the cryo-EM structures of a gp55-dependent RNA polymerase (RNAP)-promoter open complex and of an intact gp45-dependent transcription activation complex.

    • Jing Shi
    • , Aijia Wen
    •  & Yu Feng

  • Article
    | Open Access

    The BCL-2 family protein BAX functions to regulate mitochondria-driven cell death. Here the authors show that the drug Eltrombopag inhibits BAX and prevents apoptosis induced by cytotoxic stimuli.

    • Adam Z. Spitz
    • , Emmanouil Zacharioudakis
    •  & Evripidis Gavathiotis

  • Article
    | Open Access

    The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.

    • Tomoaki Kawakami
    • , Long-Jiang Yu
    •  & Zheng-Yu Wang-Otomo

  • Article
    | Open Access

    Photosystems (PS) I and II undergo state transitions to optimize photosynthesis and photoprotection. Here the authors report a cryo-electron microscopy structure of the state 2 PSI-LHCI-LHCII supercomplex from C. reinhardtii revealing subunit organization and possible pathways of energy transfer.

    • Zihui Huang
    • , Liangliang Shen
    •  & Guangye Han

  • Article
    | Open Access

    Pentameric ligand-gated ion channels (pLGICs) are key players in neurotransmission and have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. Here, the authors report structures of the pLGIC 5-HT3A serotonin receptor reconstituted into lipid bilayer discs and reveal lipid–protein interactions as well as asymmetric activation of the homopentameric receptor.

    • Yingyi Zhang
    • , Patricia M. Dijkman
    •  & Mikhail Kudryashev

  • Article
    | Open Access

    The most advanced P. falciparum circumsporozoite protein (PfCSP)-based malaria vaccine confers partial protection. Here, Pholcharee et al. present crystal structures, binding affinities/kinetics, and in vivo protection of 8 anti-NANP antibodies to understand in vivo protection of PfCSP-targeting antibodies.

    • Tossapol Pholcharee
    • , David Oyen
    •  & Ian A. Wilson

  • Article
    | Open Access

    Once DNA breaks occur, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other DNA repair factors to initiate the repair process. Here, the authors resolve the crystal structures of mouse and human HPF1, and human HPF1/PARP1 complex proving insights into PARP1 regulation.

    • Fa-Hui Sun
    • , Peng Zhao
    •  & Cai-Hong Yun

  • Article
    | Open Access

    Systemic AA amyloidosis is a protein misfolding disease caused by the formation of amyloid fibrils from serum amyloid A (SAA) protein. Here, the authors present the cryo-EM structures of AA amyloid fibrils isolated from mouse tissue and in vitro formed fibrils, which differ in their structures and they also show that the ex vivo fibrils are more resistant to proteolysis than the in vitro fibrils and propose that pathogenic amyloid fibrils might originate from proteolytic selection.

    • Akanksha Bansal
    • , Matthias Schmidt
    •  & Marcus Fändrich

  • Article
    | Open Access

    The Hsp70/Hsp40 system plays an important role in maintaining cellular proteostasis but so far it is not well understood how Hsp70 proteins are recruited to specific Hsp40 co-chaperones. Here, the authors combine biochemical and biophysical approaches to characterise the oligomeric mammalian Hsp40 DnaJB8. They identify an intra-oligomer DnaJB8 interaction between the N-terminal J-Domain and the C-terminal domain that occludes the J-Domain surface that binds Hsp70 and propose a model for DnaJB8-Hsp70 recruitment.

    • Bryan D. Ryder
    • , Irina Matlahov
    •  & Lukasz A. Joachimiak

  • Article
    | Open Access

    Aspartate transcarbamoylase acts in de novo pyrimidine biosynthesis and in plants is regulated by feedback inhibition via uridine 5-monophosphate (UMP). Here Bellin et al. describe the structural basis for this feedback inhibition, showing that UMP blocks the active site by binding to a plant specific UMP recognition loop.

    • Leo Bellin
    • , Francisco Del Caño-Ochoa
    •  & Santiago Ramón-Maiques

  • Article
    | Open Access

    Coiled-coil protein origami is a strategy for the de novo design of polypeptide nanostructures based on coiled-coil dimer forming peptides, where a single chain protein folds into a polyhedral cage. Here, the authors design a single-chain triangular bipyramid and also demonstrate that the bipyramid can be self-assembled as a heterodimeric complex, comprising pre-defined subunits.

    • Fabio Lapenta
    • , Jana Aupič
    •  & Roman Jerala

  • Article
    | Open Access

    Spindlin1 is an epigenetic reader that facilitates ribosomal RNA transcription. Here the authors reveal in vitro and structural evidence suggesting that Spindlin1 acts together with C11orf84 to recognize noncanonical bivalent mark of trimethylated lysine 4 and lysine 9 present on histone H3 tail (H3K4me3K9me3).

    • Yongming Du
    • , Yinxia Yan
    •  & Chengmin Qian

  • Article
    | Open Access

    Coiled-coil protein origami (CCPO) is a strategy for the design of polyhedral cage-shaped protein folds based on coiled-coil (CC) dimer-forming peptides. Here, the authors show that CCPO proteins fold in a multistep process governed by the spatial distance between CC modules in the primary sequence and subsequent folding intermediates, which enables the use of identical CC modules for the CCPO tetrahedron design.

    • Jana Aupič
    • , Žiga Strmšek
    •  & Roman Jerala

  • Article
    | Open Access

    An important type of post-translational protein modification is the conversion of peptidyl amino acid into enzyme cofactor. Here, the authors report functional and structural characterization of a flavoprotein monooxygenase essential for biosynthesis of cysteine tryptophylquinone (CTQ) cofactor.

    • Toshinori Oozeki
    • , Tadashi Nakai
    •  & Toshihide Okajima

  • Article
    | Open Access

    α-Synuclein is a presynaptic protein whose aberrant aggregation is associated with Parkinson’s disease. Here, the authors show how αSynuclein-induced docking of synaptic vesicles is modulated by the lipid composition changes typically observed in neurodegeneration using an in vitro system.

    • Wing K. Man
    • , Bogachan Tahirbegi
    •  & Giuliana Fusco

  • Article
    | Open Access

    Respiratory chains generate the proton motive force used for ATP synthesis. Cryo-EM structures of functional respiratory CIII2CIV supercomplex and native CIII2 from Rhodobacter capsulatus provide insight into CIII2CIV assembly and respiratory electron transport pathways in Gram-negative bacteria.

    • Stefan Steimle
    • , Trevor van Eeuwen
    •  & Fevzi Daldal

  • Article
    | Open Access

    Systemic AL amyloidosis is a protein misfolding disease caused by the aggregation and fibrillation of immunoglobulin light chains (LCs). Here, the authors present the cryo-EM structures of λ3 LC-derived amyloid fibrils that were isolated from patient tissue and they observe structural breaks, where the two different fibril structures co-exist at different z-axial positions within the same fibril.

    • Lynn Radamaker
    • , Julian Baur
    •  & Marcus Fändrich

  • Article
    | Open Access

    Biosynthesis of the statin precursor lovastatin depends on the LovB–LovC megasynthase complex. Here, the authors present cryoEM structures of LovB–LovC and core LovB, providing structural insights into the catalytic cycle underlying lovastatin production.

    • Jialiang Wang
    • , Jingdan Liang
    •  & Zhijun Wang

  • Article
    | Open Access

    Synaptic vesicles store neurotransmitters and fuse with the pre-synaptic membrane when an action potential arrives at the nerve terminal. Here authors apply cross-linking mass spectrometry to study interactions of synaptic vesicle proteins and describe a protein network of vesicle sub-populations and functional assemblies.

    • Sabine Wittig
    • , Marcelo Ganzella
    •  & Carla Schmidt

  • Article
    | Open Access

    Fluorescent protein reporters based on GFP exist, but have intrinsic disadvantages. Here the authors incorporate pH, Ca2+ and protein–protein interaction sensing modalities into de novo designed mini-fluorescence-activating proteins (mFAPs), with increased photostability and smaller size, which bind a range of DFHBI chromophore variants.

    • Jason C. Klima
    • , Lindsey A. Doyle
    •  & David Baker

  • Article
    | Open Access

    It has been suggested that pangolin coronaviruses may be the origin of SARS-CoV-2. Here the authors show that the Pangolin-CoV spike is structurally closely related to the closed form of SARS-CoV-2 spike and exhibits similar binding properties to human and pangolin ACE2; although neither spike binds bat ACE2.

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

  • Article
    | Open Access

    Ryanodine Receptors (RyRs) release Ca2+ from the endoplasmic and sarcoplasmic reticulum. Mutations in RyR are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, a collection of cryoEM structures provides insights into the molecular consequences of MHrelated RyR mutation R615C, and how apoCaM opens RyR1.

    • Kellie A. Woll
    • , Omid Haji-Ghassemi
    •  & Filip Van Petegem

  • Article
    | Open Access

    The core FADD:Caspase-8 complex and its regulatory partners, such as the cell death inhibitor c-FLIP, coordinate cell fate. Here authors present the structure of full-length procaspase-8 in a complex with FADD and reveal how recruitment of c-FLIPS into this complex inhibits Caspase-8 activity.

    • Joanna L. Fox
    • , Michelle A. Hughes
    •  & Marion MacFarlane

  • Article
    | Open Access

    p23 is a co-chaperone of Hsp90 but its mode of action is mechanistically not well understood. Here, the authors combine in vitro and yeast in vivo assays, biochemical measurements and NMR experiments to characterize p23 and identify two conserved helical elements in the intrinsically disordered C-terminal tail of p23 that together with the folded domain of p23 regulate the Hsp90 ATPase activity and affect the binding and maturation of Hsp90 clients.

    • Maximilian M. Biebl
    • , Abraham Lopez
    •  & Johannes Buchner

  • Article
    | Open Access

    RNA and DNA polymerases need to discriminate efficiently against closely related nucleotide triphosphate substrates. Here, the authors show that a conserved Arg residue is the major determinant of selectivity against deoxyribonucleoside substrates by multisubunit RNA polymerases.

    • Janne J. Mäkinen
    • , Yeonoh Shin
    •  & Georgiy A. Belogurov

  • Article
    | Open Access

    The binding of cytoplasmic Ca2+ to the anion-selective channel TMEM16A triggers a conformational change around its binding site that is coupled to the release of a gate at the constricted neck. Here authors use cryo-EM and electrophysiology to identify three hydrophobic residues at the intracellular entrance of the neck as constituents of this gate.

    • Andy K. M. Lam
    • , Jan Rheinberger
    •  & Raimund Dutzler

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