Structure determination articles within Nature Communications

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  • Article
    | Open Access

    Cryo-electron microscopy is widely employed in structural biology and uses phase contrast imaging. Here, the authors employ electron ptychography, a quantitative phase retrieval method for high-contrast, low-dose phase imaging of cryo-state rotavirus and immature HIV-1 virus-like particles, and show that electron ptychography is more efficient for phase recovery than conventional phase contrast imaging.

    • Liqi Zhou
    • , Jingdong Song
    •  & Peng Wang

  • Article
    | Open Access

    Whole-cell catalyst-based hydroxytyrosol production is low. Here, the authors increase the efficiency of its production in E. coli by de-bottlenecking two enzymatic steps catalyzed by monooxygenase and tyramine oxidase using structure-based enzyme redesign or in vivo-directed evolution with the aid of a newly developed biosensor.

    • Jun Yao
    • , Yang He
    •  & Shuang-Yan Tang

  • Article
    | Open Access

    CKK domain containing CAMSAP/Patronins recognise and regulate microtubule (MT) minus end dynamics. Here the authors compare cryo-EM structures of MT-bound human CKK and Naegleria gruberi CKK which lacks minus-end binding preference, finding NgCKK has a different interaction with, and inability to remodel, its MT binding site, shedding light on the CAMSAP/Patronin end binding mechanism.

    • Joseph Atherton
    • , Yanzhang Luo
    •  & Carolyn A. Moores

  • Article
    | Open Access

    The transient receptor potential channel member 2 (TRPM2) ion channel has a function in redox-dependent signaling. Here the authors present the cryo-EM structures of zebrafish TRPM2 in the ligand-free form, with Ca2+ and both ADP-ribose/Ca2+ and observe two-fold symmetric quaternary structure rearrangements in the ligand-bound structures that likely represent intermediate gating states.

    • Ying Yin
    • , Mengyu Wu
    •  & Seok-Yong Lee

  • Perspective
    | Open Access

    Lack of best practice guidelines currently limits the application of metabolomics in the regulatory sciences. Here, the MEtabolomics standaRds Initiative in Toxicology (MERIT) proposes methods and reporting standards for several important applications of metabolomics in regulatory toxicology.

    • Mark R. Viant
    • , Timothy M. D. Ebbels
    •  & Ralf J. M. Weber

  • Article
    | Open Access

    Human antibodies cross-reactive for several viruses within the Ebolavirus genus have been identified. Here the authors present the crystal structure of such a neutralizing monoclonal antibody (mAb) targeting the stalk of Bundibugyo virus glycoprotein and show that mAb binding may interfere with trimeric bundle assembly and/or the viral membrane.

    • Liam B. King
    • , Brandyn R. West
    •  & Erica Ollmann Saphire

  • Article
    | Open Access

    Adenovirus based (AdV) vectors are promising platforms for therapeutics and vaccines, but receptor usage of serotypes in clinical development remains unclear. Here, based on crystal structures and modeling, Baker et al. show that HAdV-D26/48 fiber knob protein interacts weakly with CAR but not with CD46 or DSG2.

    • Alexander T. Baker
    • , Alexander Greenshields-Watson
    •  & Alan L. Parker

  • Article
    | Open Access

    Quaternary contacts mediated by an extended heavy-chain framework region 3 (FR3) have been shown to improve binding to HIV envelope and virus neutralization for a few antibodies. Here, Liu et al. engraft such an FR3 loop onto several potent broadly neutralizing antibodies, resulting in improved neutralization activity and pharmacokinetics.

    • Qingbo Liu
    • , Yen-Ting Lai
    •  & Paolo Lusso

  • Article
    | Open Access

    The interactions of lignin with polysaccharides in plant secondary cell walls are not well understood. Here the authors employ solid-state NMR measurements to analyse intact stems of maize, Arabidopsis, switchgrass and rice and observe that lignin self-aggregates and forms highly hydrophobic microdomains that make extensive surface contacts to xylan.

    • Xue Kang
    • , Alex Kirui
    •  & Tuo Wang

  • Article
    | Open Access

    Eukaryotic transcription requires passage of RNA polymerase II (Pol II) through chromatin, which is impaired by nucleosomes. Here the authors report the cryo-EM structure of transcribing Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å, providing insights into the mechanism of chromatin transcription.

    • Lucas Farnung
    • , Seychelle M. Vos
    •  & Patrick Cramer

  • Article
    | Open Access

    Mutations within immunological epitope containing regions of influenza A virus can impair the established immune response between influenza strains and could impact rational vaccine design. Here Grant et al. examine the presence, structural impact and cross reactivity of two human immunodominant influenza epitope variants.

    • Emma J. Grant
    • , Tracy M. Josephs
    •  & Katherine Kedzierska

  • Article
    | Open Access

    TssA is an important component of the bacterial type VI secretion system (T6SS). Here, Dix et al. integrate structural, phylogenetic and functional analysis of the TssA subunits, providing new insights into their role in T6SS assembly and function.

    • Samuel R. Dix
    • , Hayley J. Owen
    •  & Mark S. Thomas

  • Article
    | Open Access

    Current Förster resonance energy transfer (FRET)-based fluorescence spectroscopy methods are suffering from some limitations in the field of structural biology. Here, the authors present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function.

    • Antonios Pantazis
    • , Karin Westerberg
    •  & Riccardo Olcese

  • Article
    | Open Access

    The determination of high resolution structures of G protein coupled receptors (GPCRs) in complex with heterotrimeric G proteins is challenging. Here authors develop an antibody fragment, mAB16, which stabilizes GPCR/G-protein complexes and facilitates the application of high resolution cryo-EM.

    • Shoji Maeda
    • , Antoine Koehl
    •  & Brian K. Kobilka

  • Article
    | Open Access

    Conventional reconstruction methods used in cryo-EM single particle analysis do not take the depth of field effect into account. Here the authors present a block-based reconstruction method to deal with the depth of field effect and show that this approach can improve the resolution of cryo-EM virus structures.

    • Dongjie Zhu
    • , Xiangxi Wang
    •  & Xinzheng Zhang

  • Article
    | Open Access

    BMI1, a core element of the polycomb repressive complex 1, is suggested to have oncogenic activity in a variety of cancers. Here, the authors report the structure of BMI1 bound to the protein PHC2, identify BMI1 homo-oligomerization interfaces, and analyse the role of BMI1 protein-protein interactions in PRC1 function.

    • Felicia Gray
    • , Hyo Je Cho
    •  & Tomasz Cierpicki

  • Article
    | Open Access

    Tetrameric cationic channels specificity is determined by the sequence and structural conformation of their selectivity filter. Here, the authors show that a cationic channel from Tsukamurella paurometabola is non-selective due to a Ca2+-binding motif within its unusual proline-rich filter.

    • Balasundaresan Dhakshnamoorthy
    • , Ahmed Rohaim
    •  & Benoît Roux

  • Article
    | Open Access

    Large-scale dense reconstruction of neuronal circuits (or connectomics) requires methods for large-volume dense en-blocelectron microscopy (EM) staining. Here the authors develop a protocol for staining tissue blocks from mouse neocortex sized at least 1 mm in diameter, enabling correlated functional and structural circuit analyses.

    • Yunfeng Hua
    • , Philip Laserstein
    •  & Moritz Helmstaedter

  • Article
    | Open Access

    The peptidoglycan (PG) layer of the Gram-positive bacteria cell wall resists turgor pressure, but the architecture of this layer is largely unknown. Here the authors use high resolution atomic force microscopy to image the PG layer from live Streptococcusto reveal a net-like arrangement that resists osmotic challenge by stretching and stiffening.

    • Ron Saar Dover
    • , Arkady Bitler
    •  & Yechiel Shai

  • Article
    | Open Access

    The determination of RNA structures within high-molecular weight protein-RNA complexes in non-crystalline state is technically challenging. Here, the authors describe a solid-state NMR protocol for the determination of RNA structures at high resolution.

    • Alexander Marchanka
    • , Bernd Simon
    •  & Teresa Carlomagno

  • Article |

    High-resolution structures of large RNAs and protein–RNA complexes are difficult to solve due to inherent structural flexibility and a high risk of crystallization artefacts. Here, Duss et al. present a novel EPR-based approach to aid structure determination of large RNAs and protein–RNA complexes in solution.

    • Olivier Duss
    • , Maxim Yulikov
    •  & Frédéric H.-T. Allain

  • Article |

    RNA is central to many cellular functions, but in vivo structures of most RNAs are unknown. Here Kwok et al. present a universally applicable method, DMS/SHAPE-LMPCR, to identify structures of low-abundance transcripts in living cells, which reveals important features that are uniquely present in vivo.

    • Chun Kit Kwok
    • , Yiliang Ding
    •  & Philip C Bevilacqua

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