Structural biology articles within Nature

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  • Article |

    X-ray crystal structures are presented of the N-methyl-d-aspartate (NMDA) receptor, a calcium-permeable ion channel that opens upon binding of glutamate and glycine; glutamate is a key excitatory neurotransmitter and enhanced structural insight of this receptor may aid development of therapeutic small molecules.

    • Chia-Hsueh Lee
    • , Wei Lü
    •  & Eric Gouaux

  • News & Views |

    Two crystal structures of the LptD–LptE protein complex reveal how the cell-wall component lipopolysaccharide is delivered and inserted into the external leaflet of the bacterial outer membrane. See Article p.52 & Letter p.108

    • Russell E. Bishop

  • News & Views |

    Many enzymes form 'assembly lines' containing a series of catalytic modules. Visualization of how the structure of a module shifts during catalysis provides a clearer idea of how such enzymes work. See Article p.512 & Letter p.560

    • Peter F. Leadlay

  • Letter |

    Lipopolysaccharide, an essential component of the Gram-negative bacteria outer membrane, is inserted by LptD–LptE, a protein complex with a unique ‘barrel and plug’ architecture; the structure of the LptD–LptE complex of Shigella flexneri determined here shows LptD forming a 26-stranded β-barrel with LptE located inside the barrel of LptD, the first two β-strands are distorted by two proline residues, creating a potential portal in the barrel wall that might allow lateral diffusion of lipopolysaccharide into the outer membrane.

    • Shuai Qiao
    • , Qingshan Luo
    •  & Yihua Huang

  • Article |

    Lipopolysaccharide, an essential component of the outer membranes of Gram-negative bacteria, is inserted by LptD–LptE, a protein complex with a unique ‘barrel and plug’ architecture; the structure, molecular dynamics simulations and functional assays of the LptD–LptE complex of Salmonella typhimurium suggest that lipopolysaccharide may pass through the barrel and is then inserted into the outer leaflet of the outer membrane through a lateral opening between two β-strands of LptD.

    • Haohao Dong
    • , Quanju Xiang
    •  & Changjiang Dong

  • Letter |

    Polyketide synthases (PKSs) are multidomain enzymes that produce polyketides, which form the basis of many therapeutic agents; here, electron cryo-microscopy is used to probe the structure of an intact module of a multi-enzyme PKS in different functional states.

    • Jonathan R. Whicher
    • , Somnath Dutta
    •  & Georgios Skiniotis

  • Article |

    Polyketide synthases are multidomain enzymes that produce polyketides, which form the basis of many therapeutic agents; here, electron cryo-microscopy is used to establish the structure of a bacterial full-length module, and to elucidate the structural basis of both intramodule and intermodule substrate transfer.

    • Somnath Dutta
    • , Jonathan R. Whicher
    •  & Georgios Skiniotis

  • News & Views |

    Enzymes that attach amino acids to transfer RNAs during protein synthesis must recognize both substrates specifically. Crystal structures reveal a mechanism that explains the RNA specificity for one such system. See Article p.507

    • Oscar Vargas-Rodriguez
    •  & Karin Musier-Forsyth

  • Article |

    GABAA receptors are the principal mediators of rapid inhibitor synaptic transmission in the brain, and a decline in GABAA signalling leads to diseases including epilepsy, insomnia, anxiety and autism; here, the first X-ray crystal structure of a human GABAA receptor, the human β3 homopentamer, reveals structural features unique for this receptor class and uncovers the locations of key disease-causing mutations.

    • Paul S. Miller
    •  & A. Radu Aricescu

  • Letter |

    RNA molecules can perform multiple functions, which can be driven by different conformational states; here, the crystal structure of the transfer-RNA-like structure of the turnip yellow mosaic virus is solved, providing insight into the structural basis of RNA multifunctionality.

    • Timothy M. Colussi
    • , David A. Costantino
    •  & Jeffrey S. Kieft

  • Letter |

    A new mass-spectrometry method has been developed to obtain high-resolution spectra of folded proteins bound to lipids; using this technique as well as X-ray crystallography provides evidence for membrane protein conformational change as a result of lipid–protein interaction.

    • Arthur Laganowsky
    • , Eamonn Reading
    •  & Carol V. Robinson

  • Article |

    The structure of human GLUT1 in an inward-open conformation is reported; access to the structure of the human protein, instead of just a bacterial homologue, made it possible to map (inactivating) mutations associated with GLUT1 deficiency syndrome onto the structure.

    • Dong Deng
    • , Chao Xu
    •  & Nieng Yan

  • Editorial |

    It has been no small feat for the Protein Data Bank to stay relevant for 100,000 structures.

  • Letter |

    Crystal structures of human and prokaryotic ribosomal oxygenases reported here, with and without their ribosomal protein substrates, support their assignments as hydroxylases, and provide insights into the evolution of the JmjC-domain-containing hydroxylases and demethylases.

    • Rasheduzzaman Chowdhury
    • , Rok Sekirnik
    •  & Christopher J. Schofield

  • Letter |

    This study shows how the yeast Ctf4 protein couples the DNA helicase, Cdc45–MCM–GINS, to DNA polymerase α — the GINS subunit of the helicase and the polymerase use a similar interaction to bind Ctf4, suggesting that, as Ctf4 is a trimer, two polymerases could be simultaneously coupled to a single helicase during lagging-strand synthesis.

    • Aline C. Simon
    • , Jin C. Zhou
    •  & Luca Pellegrini

  • News & Views |

    A tour de force of X-ray scattering has yielded structures of a phytochrome photoreceptor in its dark and illuminated states, showing how localized protein refolding magnifies a light signal to form a cellular message. See Letter p.245

    • Anna W. Baker
    •  & Katrina T. Forest

  • Letter |

    The solution and crystal structures of a bacterial phytochrome photosensory core in both its resting and activated states are determined; switching between closed (resting) and open (activated) forms is found to be mediated by a conserved ‘tongue’, and the structures indicate that smaller changes in the vicinity of the chromophore are amplified in scale as they are transmitted through the tongue and beyond.

    • Heikki Takala
    • , Alexander Björling
    •  & Sebastian Westenhoff

  • Letter |

    An X-ray structure of human P2Y12 receptor, a clinical drug target for platelet aggregation inhibitors, is presented in complex with an agonist, providing insight into the δ-group of class A G-protein-coupled receptors.

    • Jin Zhang
    • , Kaihua Zhang
    •  & Qiang Zhao

  • Letter |

    Many bacteria are able to survive in the presence of antibiotics in part because they possess pumps that can remove a broad range of small molecules; here, the structure of one such pump, AcrAB–TolC, is determined using X-ray crystallography and cryo-electron microscopy.

    • Dijun Du
    • , Zhao Wang
    •  & Ben F. Luisi

  • Letter |

    The crystal structure of the bacterial protein YidC is reported, together with a structure-based functional analysis, providing insight into the role of YidC in inserting single-spanning membrane proteins into the membrane.

    • Kaoru Kumazaki
    • , Shinobu Chiba
    •  & Osamu Nureki

  • News & Views |

    The structure of a photosynthetic complex from a purple bacterium reveals a new class of light-harvesting protein and the channels that might allow electron-transporting molecules to escape this otherwise closed system. See Article p.228

    • Richard J. Cogdell
    •  & Aleksander W. Roszak

  • Article |

    The near-atomic-level structure of a complete bacterial light-harvesting antenna–reaction centre (LH1–RC) complex is described here; the structure reveals how energy is transferred from the LH1 to the RC in a highly efficient way and suggests how ubiquinone might cross a closed LH1 barrier.

    • Satomi Niwa
    • , Long-Jiang Yu
    •  & Kunio Miki

  • Letter |

    A dual-function helicase–nuclease, typified by RecBCD in Escherichia coli, acts on free DNA ends during bacterial double-stranded break repair until it reaches a χ sequence at which it pauses before continuing with modified enzymatic properties; here several crystal structures of the related AddAB enzyme from Bacillus subtilis bound to χ-containing DNA are presented, offering insight into χ recognition and its effect on DNA translocation.

    • Wojciech W. Krajewski
    • , Xin Fu
    •  & Dale B. Wigley

  • Letter |

    A set of parameters based on the response of a molecule’s properties to infrared vibrations can be used to model and predict selectivity trends for molecular reactions with interlinked steric and electronic effects at positions of interest

    • Anat Milo
    • , Elizabeth N. Bess
    •  & Matthew S. Sigman

  • Letter |

    The three-dimensional structure of the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid.

    • Harry H. Low
    • , Francesca Gubellini
    •  & Gabriel Waksman

  • Letter |

    RIG-I protein recognizes viral duplex RNA with a 5′-triphosphate group, activating innate immune responses; a crystal structure of its tetrameric CARD signalling domain reveals that non-covalently linked ubiquitin chains stabilize the tetramer in a ‘lock-washer’ structure that serves as a signalling platform for the recruitment and activation of MAVS.

    • Alys Peisley
    • , Bin Wu
    •  & Sun Hur

  • News & Views |

    The protein NRT1.1 transports nitrate ions into plants over a wide range of concentrations. Two studies provide structural insight into this unusual behaviour, but give different explanations for it. See Articles p.68 & p.73

    • Yi-Fang Tsay

  • Article |

    In Arabidopsis thaliana the phosphorylation state of the ‘dual affinity’ transporter, NRT1.1, allows the uptake of nitrate over a wide concentration range; the crystal structure and molecular basis for this is described in this study.

    • Joanne L. Parker
    •  & Simon Newstead

  • Article |

    High-resolution structures of the Photorhabdus luminescens TcA toxin subunit and the entire Tc toxin complex reveal important new insights into Tc complex structure and function.

    • Dominic Meusch
    • , Christos Gatsogiannis
    •  & Stefan Raunser

  • Letter |

    Nascent secretory and membrane proteins are targeted to the Sec61 protein-conducting channel for translocation across or insertion into the endoplasmic reticulum membrane; here cryo-electron microscopy structures of eukaryotic ribosome–channel complexes show how this channel opens vertically during translocation of a secretory protein into the lumen of the endoplasmic reticulum and how it opens laterally during insertion of a transmembrane domain into the lipid bilayer.

    • Marko Gogala
    • , Thomas Becker
    •  & Roland Beckmann

  • Article |

    Computational protein design methods are used to generate new candidates for a human respiratory syncytial virus (RSV) vaccine; artificial protein scaffolds that mimic the structure of a RSV epitope are shown to induce RSV-specific neutralizing antibodies in macaques.

    • Bruno E. Correia
    • , John T. Bates
    •  & William R. Schief

  • Comment |

    Georgina Ferry celebrates the egalitarian, collaborative culture that has so far produced two female Nobel prizewinners.

    • Georgina Ferry

  • News & Views |

    Synchrotrons have long been the preferred X-ray sources for crystallography, but competition has arrived with the advent of X-ray free-electron lasers. A synchrotron expert and an advocate of free-electron lasers discuss the prospects of the respective source types for applications in structural biology.

    • Sean McSweeney
    •  & Petra Fromme

  • Article |

    The 1.8 Å high-resolution X-ray crystal structure of the human δ-opioid receptor is presented, with site-directed mutagenesis and functional studies revealing a crucial role for a sodium ion in mediating allosteric control in this receptor.

    • Gustavo Fenalti
    • , Patrick M. Giguere
    •  & Raymond C. Stevens

  • News & Views |

    Two crystal structures reveal that the Vif and Vpx proteins of human and simian immunodeficiency viruses mediate evasion of host defences by reprogramming the cellular protein-degradation machinery. See Letters p.229 & p.234

    • Michael H. Malim

  • Letter |

    The Tet family of dioxygenase enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, which has an effect on gene expression; here the structure of NgTet1, a Tet-like protein with the same activity as mammalian Tet1, is determined, showing that NgTet1 uses a base-flipping mechanism to access 5-methylcytosine.

    • Hideharu Hashimoto
    • , June E. Pais
    •  & Xiaodong Cheng

  • Letter |

    A highly specific chemical crosslinking method is used to trap a complex between an acyl carrier protein and a fatty acid dehydratase during fatty acid biosynthesis; subsequent X-ray crystallography, NMR spectroscopy and molecular dynamics simulations techniques enable the detailed study of this complex.

    • Chi Nguyen
    • , Robert W. Haushalter
    •  & Michael D. Burkart

  • Article |

    Cryo-electron microscopy combined with chemical crosslinking and mass spectrometry is used to determine the structure of the large subunit of the mammalian mitoribosome; this structure provides detailed structural insight, particularly of the molecular architecture of the polypeptide exit site, which has been structurally remodelled during evolution, presumably to help facilitate the membrane insertion of the highly hydrophobic proteins encoded by the mitochondrial genome.

    • Basil J. Greber
    • , Daniel Boehringer
    •  & Nenad Ban

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