Structural biology articles within Nature Communications

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  • Article |

    The hepatitis C virus RNA genome is translated via an internal ribosome entry site. Pérard et al. present an atomic model of this site, and using molecular dynamics simulations, identify conformational flexibility that may underlie its function during translation initiation.

    • Julien Pérard
    • , Cédric Leyrat
    •  & Marc Jamin

  • Article |

    The post-translational protein modification tyrosine sulfation is catalysed by tyrosylprotein sulfotransferase (TPST). Teramoto et al. present the first crystal structure of the human TPST isoform 2 complexed with a substrate peptide derived from complement C4 and 3′phosphoadenosine-5′-phosphate, revealing the molecular basis of catalysis.

    • Takamasa Teramoto
    • , Yukari Fujikawa
    •  & Yoshimitsu Kakuta

  • Article |

    The bacterial tetracycline resistance protein Tet(O) binds to the ribosome, preventing tetracycline from inhibiting translation. Using cryo-electron microscopic reconstruction, the authors present an atomic model of Tet(O) bound to the 70S ribosome, and reveal how Tet(O) promotes antibiotic resistance.

    • Wen Li
    • , Gemma C. Atkinson
    •  & Joachim Frank

  • Article |

    The bullet shape of Rhabdoviruses is thought to depend on their matrix protein, which stabilizes the nucleocapsid coil. Desfosses and colleagues show that the nucleoprotein of the vesicular stomatitis virus can fold the genome into a bullet-shaped skeleton in the absence of other viral components.

    • Ambroise Desfosses
    • , Euripedes A. Ribeiro Jr
    •  & Irina Gutsche

  • Article
    | Open Access

    RNase P is a key enzyme implicated in transfer RNA maturation that removes the 5′-leader sequences from transfer RNA precursors. In this study, a biophysical characterization of a novel protein-only variant of RNase P, known as PRORP (PROteinaceous RNase P), reveals that transfer RNA recognition by PRORP is similar to that by ribonucleoprotein RNase P.

    • Anthony Gobert
    • , Franziska Pinker
    •  & Philippe Giegé

  • Article |

    The antibiotic streptomycin increases errors in protein translation, but it is unclear how streptomycin exerts its effect on the ribosome. Demirci et al. present X-ray crystal structures that reveal conformational changes induced by streptomycin, which may inspire future efforts in antibiotics design.

    • Hasan Demirci
    • , Frank Murphy IV
    •  & Gerwald Jogl

  • Article
    | Open Access

    How the genome is physically organized is less understood in archaea than in eubacteria or eukaryotes. Laurens et al. measure DNA binding by the Sulfolobus solfataricusproteins Alba1 and Alba2 using single-molecule techniques and conclude that the presence of Alba2 leads to more bridging between DNA.

    • Niels Laurens
    • , Rosalie P.C. Driessen
    •  & Gijs J.L. Wuite

  • Article
    | Open Access

    Proteins are integrated into cellular membranes either co-translationally through Sec/SRP or post-translationally by chaperones. These authors show that an integration-dedicated chaperone inE. coli, MPIase, is a glycolipid and facilitates protein insertion into the inner membrane of the bacterium.

    • Ken-ichi Nishiyama
    • , Masahide Maeda
    •  & Keiko Shimamoto

  • Article
    | Open Access

    Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al.report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel.

    • Emily C. McCusker
    • , Claire Bagnéris
    •  & B.A. Wallace

  • Article |

    The iron–sulphur enzyme IspH catalyses the final step of the methylerythritol phosphate isoprenoid biosynthesis pathway. Spanet al. report that IspH can hydrate acetylenes to aldehydes and ketones, in addition to its role as a 2H+/2e−reductase.

    • Ingrid Span
    • , Ke Wang
    •  & Michael Groll

  • Article |

    Resilin is a polymeric elastic protein that is important for the flight and jumping of insects. Here, the structure-function relationships ofDrosophilaresilin are investigated, and a mechanical model is proposed to account for its elasticity.

    • Guokui Qin
    • , Xiao Hu
    •  & David L. Kaplan

  • Article
    | Open Access

    The activity of the Acid sensing ion channel 1, ASIC1, can be modulated by the gating modifier Psalmotoxin 1 but the molecular mechanism is unclear. Dawsonet al. report the structure of chicken ASIC1 bound to Psalmotoxin 1 and find that the toxin locks two regulatory regions of the channel into a desensitized conformation.

    • Roger J.P. Dawson
    • , Jörg Benz
    •  & Armin Ruf

  • Article |

    Nucleic acid superstructures are required to package genomes into the nucleus of cells. In this study, the superstructure of an RNA supercoil species is reported and is shown to be dependent on an RNA-binding protein that induces a higher level of organization compared with DNA superstructures.

    • Jason R. Stagno
    • , Buyong Ma
    •  & Xinhua Ji

  • Article |

    Poly(ADP-ribose) glycohydrolase catabolises poly(ADP-ribose), which is covalently attached to proteins following post-translational modification. In this study, the structure of poly(ADP-ribose) glycohydrolase fromTetrahymena thermophilais reported in complex with the small molecule inhibitor RBPI-3.

    • Mark S. Dunstan
    • , Eva Barkauskaite
    •  & Ivan Ahel

  • Article |

    Processes that regulate the mechanical and dynamic properties of actin cytoskeleton are important for multiple eukaryotic cell functions. In this study, using reconstituted crosslinked actin networks, organization is found to be determined by the competing kinetics of actin gelation and bundle formation.

    • Tobias T. Falzone
    • , Martin Lenz
    •  & Margaret L. Gardel

  • Article |

    Fanconi's anaemia is characterized by an inability to repair DNA damage and is associated with mutations in the Fanconi anaemia nuclear complex, which includes the protein FANCM. This study reports the crystal structures of a fragment of FANCM bound to the histone-fold-containing protein complex, MHF1–MHF2.

    • Yuyong Tao
    • , Changjiang Jin
    •  & Maikun Teng

  • Article
    | Open Access

    The pentameric ligand gated ion channel fromErwinia chrysanthemi(ELIC) is similar in structure to the nicotinic acetylcholine receptor, a member of the Cys-loop receptor family. This study reports the crystal structure of ELIC bound to acetylcholine and shows that acetylcholine is a competitive antagonist of ELIC.

    • Jianjun Pan
    • , Qiang Chen
    •  & Pei Tang

  • Article |

    Perturbation of the cardiac voltage-gated sodium channel, NaV1.5, by drugs or inherited mutation can underlie and trigger cardiac arrhythmias. Here, the role of the NaV1.5 carboxy terminus in channel inactivation is investigated, and structural details of an arrhythmia associated H6 mutant are reported.

    • Ian W. Glaaser
    • , Jeremiah D. Osteen
    •  & Robert S. Kass

  • Article
    | Open Access

    The peripheral stalks of rotary ATPases counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Stewartet al.report the crystal structure of an A-type ATPase/synthase peripheral stalk and identify bending and twisting motions that permit the radial wobbling of the headgroup.

    • Alastair G. Stewart
    • , Lawrence K. Lee
    •  & Daniela Stock

  • Article
    | Open Access

    Beclin1 is a key regulator of VPS34-related processes, including autophagy. Liet al. solve the crystal structure of Beclin 1 CC domain, an antiparallel dimer that is rendered metastable by a series of a-d' pairings, which determines its ability to form distinct heterodimers either with Atg14L or UVRAG.

    • Xiaohua Li
    • , Liqiang He
    •  & Yanxiang Zhao

  • Article
    | Open Access

    The influenza A virus genome consists of eight RNA segments, which permits genetic reassortment and contributes to the emergence of novel strains with pandemic potential. Here, electron tomography is used to study the three-dimensional structure of ribonucleoprotein complexes within progeny virions.

    • Takeshi Noda
    • , Yukihiko Sugita
    •  & Yoshihiro Kawaoka

  • Article |

    Inward rectifier potassium channels are regulated by a range of ligands that act on a common gate, but the structural details of gating are unclear. Here, the molecular motions associated with gating of KirBac1.1 channels are assessed using small molecule fluorescent probes attached to introduced cysteines.

    • Shizhen Wang
    • , Sun-Joo Lee
    •  & Colin G. Nichols

  • Article
    | Open Access

    Albumin transport proteins circulate in the blood and are protected from degradation by interaction with the neonatal Fc receptor. Andersenet al. investigate the albumin binding site of the neonatal Fc receptor and find pH sensitive ionic networks at the binding interface.

    • Jan Terje Andersen
    • , Bjørn Dalhus
    •  & Inger Sandlie

  • Article |

    Herpesvirus glycoprotein D binds to nectin 1 and the herpes virus entry mediator protein on the surface of host cells. In this study, Zhanget al. report the crystal structure of glycoprotein D in complex with the immunoglobulin-like domains of nectin 1, which suggests that binding of glycoprotein D to nectin 1 prevents nectin 1 dimerization.

    • Na Zhang
    • , Jinghua Yan
    •  & George F Gao

  • Article |

    The inhibitor of apoptosis protein DIAP1 exists in an auto-inhibited conformation, but the details of its molecular interactions are poorly understood. Here, crystal structures reveal the auto-inhibition mechanism of DIAP1 and show how the active form of the protein binds to the effector caspase drICE.

    • Xiaochun Li
    • , Jiawei Wang
    •  & Yigong Shi

  • Article |

    Thioredoxin reductase 1 is a flavoprotein that is involved in the regulation of redox homeostasis. Fritz-Wolfet al. report the first crystal structures of thioredoxin reductase 1 in complex with its substrate, thioredoxin, and confirm that the enzyme uses a flexible carboxy-terminal arm for electron transport to its substrates.

    • Karin Fritz-Wolf
    • , Sebastian Kehr
    •  & Katja Becker

  • Article
    | Open Access

    von Willebrand factor (VWF) multimers mediate primary adhesion and aggregation of platelets. Jakobiet al. reveal a calcium-binding site in the VWF-A2 domain, and show that calcium binding encourages folding of the protein and has a role in mechanosensing.

    • Arjen J. Jakobi
    • , Alireza Mashaghi
    •  & Eric G. Huizinga

  • Article |

    N-methyl-D-aspartate receptors mediate excitatory synaptic transmission, and those containing GluN2D subunits have an unusually long deactivation time. Vance et al. show that the conformational variability of the ligand-binding domain and the structure of the activating ligand influence deactivation time.

    • Katie M. Vance
    • , Noriko Simorowski
    •  & Hiro Furukawa

  • Article
    | Open Access

    Cathepsin L mediates proteolysis of the histone H3 tail and is a factor in cell-cycle progression and cellular differentiation. Adams-Cioabaet al. report crystal structures of an inactive mutant of the protease complexed with substrate peptides, and find that it is highly accommodating of modified substrates.

    • Melanie A. Adams-Cioaba
    • , Joanne C. Krupa
    •  & Jinrong Min

  • Article
    | Open Access

    Cryptophane-A is a prototypical organic host molecule that binds reversibly to neutral guest molecules. Taratulaet al.report X-ray structures of cryptophane-A complexed with a range of host molecules to show that the cryptophane host–guest system exhibits ‘induced fit’.

    • Olena Taratula
    • , P. Aru Hill
    •  & Ivan J. Dmochowski

  • Article
    | Open Access

    The influenza virus life cycle relies on sialidases, which are classified as group-1 or group-2, depending on the flexibility of the '150-loop'. In this study, chemical compounds are developed, which lock open the '150-loop', selectively inhibiting the activity of group-1 sialidases.

    • Santosh Rudrawar
    • , Jeffrey C. Dyason
    •  & Mark von Itzstein

  • Article
    | Open Access

    Frataxin is an essential protein that has been linked to iron–sulphur cluster assembly, and reduced levels are associated with Friedrich's ataxia. In this study, a combination of techniques is used to probe the interactions of the bacterial frataxin orthologue CyaY with the iron–sulphur cluster assembly machinery.

    • Filippo Prischi
    • , Petr V. Konarev
    •  & Annalisa Pastore

  • Article
    | Open Access

    A recent X-ray structure revealed the closed state of a P2X receptor ion channel. Here, Li and colleagues probe the structural rearrangements that take place during channel opening by measuring the effects of covalent modification of engineered cysteines.

    • Mufeng Li
    • , Toshimitsu Kawate
    •  & Kenton J. Swartz

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