Bacterial structural biology articles within Nature

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  • Article
    | Open Access

    Cryo-electron tomography is used to reveal the structural dynamics and functional diversity of translating ribosomes in Mycoplasma pneumoniae, providing insight into the translation elongation cycle inside cells and how it is reshaped by antibiotics.

    • Liang Xue
    • , Swantje Lenz
    •  & Julia Mahamid

  • Article |

    A bacterial antiviral defence system generates a cyclic tri-adenylate that binds to a TIR–SAVED effector, inducing formation of a superhelical structure with adjacent TIR domains organizing into an active site, allowing NAD+ degradation.

    • Gaëlle Hogrel
    • , Abbie Guild
    •  & Malcolm F. White

  • Article |

    Cryo-electron microscopy structures of the bacterial O-antigen ligase WaaL, combined with genetics, biochemistry and molecular dynamics simulations, provide insight into the mechanism by which WaaL catalyses the biosynthesis of lipopolysaccharide.

    • Khuram U. Ashraf
    • , Rie Nygaard
    •  & Filippo Mancia

  • Article
    | Open Access

    A cryo-electron microscopy structure of the inner membrane complex of the ESX-5 type VII secretion system of Mycobacterium tuberculosis reveals an important role of interactions with MycP5 protease for complex integrity.

    • Catalin M. Bunduc
    • , Dirk Fahrenkamp
    •  & Thomas C. Marlovits

  • Article |

    X-ray crystallography and cryo-electron microscopy structures of the transcriptional repressor of the methylomycin gene cluster, MmfR, reveal the molecular basis for regulation of antibiotic biosynthesis by AHFCA hormones in Actinobacteria.

    • Shanshan Zhou
    • , Hussain Bhukya
    •  & Christophe Corre

  • Article |

    Structural analyses of the type III CRISPR accessory protein Card1, which induces dormancy in infected hosts to provide immunity against phage infection, reveal the mechanisms by which it cleaves single-stranded RNA and DNA.

    • Jakob T. Rostøl
    • , Wei Xie
    •  & Luciano A. Marraffini

  • Article |

    The authors report near-atomic resolution structures of the R-type bacteriocin from Pseudomonas aeruginosa in the pre-contraction and post-contraction states, and these structures provide insight into the mechanism of action of molecular syringes.

    • Peng Ge
    • , Dean Scholl
    •  & Z. Hong Zhou

  • Article |

    Cryo-electron microscopy structures of LptB2FGC, in nucleotide-free and vanadate-trapped states, reveal the mechanism of lipopolysaccharide extraction from the inner membrane of Gram-negative bacteria and a role for LptC in efficient lipopolysaccharide transport.

    • Yanyan Li
    • , Benjamin J. Orlando
    •  & Maofu Liao

  • Article |

    Cryo-electron microscopy snapshots of the E. coli flippase MsbA at discrete functional states reveal a ‘trap and flip’ mechanism for lipopolysaccharide flipping and the conformational transitions of MsbA during its substrate transport cycle.

    • Wei Mi
    • , Yanyan Li
    •  & Maofu Liao

  • Letter |

    The structure of the bacterial 70S ribosome in complex with ArfA, the release factor RF2, a short non-stop mRNA and a cognate P-site tRNA is presented, revealing how ArfA and RF2 facilitate alternative translation termination of the non-stop ribosomal complex using a stop-codon surrogate mechanism.

    • Chengying Ma
    • , Daisuke Kurita
    •  & Ning Gao

  • Letter |

    The structure of a bacterial ribosome–RelA complex reveals that RelA, a protein recruited to the ribosome in the case of scarce amino acids, binds in a different location to translation factors, and that this binding event suppresses auto-inhibition to activate synthesis of the (p)ppGpp secondary messenger, thus initiating stringent control.

    • Alan Brown
    • , Israel S. Fernández
    •  & V. Ramakrishnan

  • Letter |

    The crystal structure of monomeric Lachnospiraceae bacterium Cpf1 protein bound to CRISPR RNA is presented, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.

    • De Dong
    • , Kuan Ren
    •  & Zhiwei Huang

  • Article |

    A combination of X-ray crystallography, electron microscopy, functional assays and time-lapse fluorescence microscopy shows that a protein of previously unknown function, TssA, forms a dodecameric complex that interacts with components of the tube and sheath of the type VI secretion system of bacteria, and that it primes and coordinates biogenesis of both the tail tube and the sheath.

    • Abdelrahim Zoued
    • , Eric Durand
    •  & Eric Cascales

  • Article |

    Two crystal structures of the Escherichia coli β-barrel assembly machinery (BAM complex) are presented, one of which includes all five subunits (BamA–BamE), in two distinct conformational states; together with functional assays and molecular dynamics stimulations, these structures help to generate a model for outer membrane protein insertion.

    • Yinghong Gu
    • , Huanyu Li
    •  & Changjiang Dong

  • Letter |

    The structure of E. coli Cascade bound to foreign target DNA is presented, revealing the basis of the relaxed Cascade PAM recognition specificity, which results from its interaction with the minor groove, and demonstrating how a wedge in Cascade forces the directional pairing of the target strand with CRISPR RNA while stabilizing the non-target displaced strand.

    • Robert P. Hayes
    • , Yibei Xiao
    •  & Ailong Ke

  • Article |

    A novel drug, ribocil, is shown to mimic the binding of a natural ligand to a bacterial riboflavin riboswitch (a non-coding stretch of messenger RNA whose structure is affected by a ligand—usually one related to the function of the protein encoded by the messenger RNA) to cause inhibition of bacterial growth; the ability to target an RNA structural element with a synthetic small molecule may expand our view of the target space susceptible to therapeutic intervention.

    • John A. Howe
    • , Hao Wang
    •  & Terry Roemer

  • Letter |

    A single particle cryo-EM structure of the 70S ribosome in complex with the elongation factor Tu breaks the 3 Å resolution barrier of the technique and locally exceeds the resolution of previous crystallographic studies, revealing all modifications in rRNA and explaining their roles in ribosome function and antibiotic binding.

    • Niels Fischer
    • , Piotr Neumann
    •  & Holger Stark

  • Letter |

    The cytosolic concentration of citrate partially depends on its direct import across the plasma membrane by the Na+-dependent citrate transporter (NaCT); here the X-ray crystal structure of a bacterial homologue of NaCT is reported, which, along with transport-activity studies, suggests how specific conformational changes facilitate substrate translocation across the cellular membrane.

    • Romina Mancusso
    • , G. Glenn Gregorio
    •  & Da-Neng Wang

  • Letter |

    The structure of the needle of the type III secretion system of Salmonella typhimurium, used to inject virulence proteins into host cells during infection, has been resolved by a combination of in vitro needle production, solid-state nuclear magnetic resonance, electron microscopy and Rosetta modelling at atomic resolution.

    • Antoine Loquet
    • , Nikolaos G. Sgourakis
    •  & Adam Lange

  • Letter |

    Gram-negative bacteria expel toxic chemicals via tripartite efflux pumps spanning both the inner and outer membranes. A crystallographic model of this tripartite efflux complex has been unavailable because co-crystallization of different components of the system has proven to be extremely difficult. The X-ray crystal structure of CusA of the CusCBA tripartite efflux system from Escherichia coli has been reported previously, and here the X-ray crystal structure of the CusBA co-complex is reported. The structure reveals that the trimeric CusA efflux pump interacts with six CusB protein molecules at the upper half of the periplasmic domain, and the predicted structure of the trimeric CusC channel was used to develop a model of for the tripartite efflux complex.

    • Chih-Chia Su
    • , Feng Long
    •  & Edward W. Yu

  • News & Views |

    The crystal structure of a protein channel provides clues about the mechanisms that control the closure of pores found in the epidermis of plant leaves. Excitingly, the protein channel folds in a way never seen before. See Article p.1074

    • Sébastien Thomine
    •  & Hélène Barbier-Brygoo

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