Structure determination articles within Nature Communications

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  • Article
    | Open Access

    Work by Klyshko and Kim et al. lays the foundation for simulating pump-probe experiments and demonstrates how the dynamic behaviour of proteins extends to the crystal environment, emphasizing the need for an ensemble view in understanding functional motions.

    • Eugene Klyshko
    • , Justin Sung-Ho Kim
    •  & Sarah Rauscher

  • Article
    | Open Access

    It has been challenging to make long RNAs with site-specific modifications for NMR study. Here the authors present SegModTeX: a method for site-specific and segmental labeling of RNAs independent of their sequence or segment length, with applications for biological- and artificial NTP analogues at purity and scale sufficient for NMR.

    • Raphael Haslecker
    • , Vincent V. Pham
    •  & Victoria M. D’Souza

  • Article
    | Open Access

    Predicting the effective assembly of a set of proteins into a desired structure has traditionally been a challenging task. Here, authors demonstrate that advancements in automatic differentiation make it possible to address this problem using classical statistical mechanics.

    • Agnese I. Curatolo
    • , Ofer Kimchi
    •  & Michael P. Brenner

  • Article
    | Open Access

    The formation of polymeric Ig complexes is important for the function of IgM and can vary between species. Here the authors structurally analyse IgM from a teleost species that doesn’t encode a joining chain, which results in a different 3D structure compared to mammalian IgM where other parts of the protein associate to form polymeric complexes.

    • Mengfan Lyu
    • , Andrey G. Malyutin
    •  & Beth M. Stadtmueller

  • Article
    | Open Access

    Here, the reaction of the suicide inhibitor sulbactam with the M. tuberculosis β-lactamase (BlaC) is investigated with time-resolved crystallography. Singular Value Decomposition is implemented to extract kinetic information despite changes in unit cell parameters during the time-course of the reaction.

    • Tek Narsingh Malla
    • , Kara Zielinski
    •  & Marius Schmidt

  • Article
    | Open Access

    TPX2 is a key factor stimulating branching microtubule (MT) nucleation. TPX2 forms condensates on MTs critical for branching. In this work, the authors report the atomic-level structure of TPX2 C-terminal minimal active domain on MT lattice and its binding interface, determined by magic-angle-spinning NMR.

    • Changmiao Guo
    • , Raymundo Alfaro-Aco
    •  & Tatyana Polenova

  • Article
    | Open Access

    Endothelin receptors (ETAR and ETBR) are critical for vasoregulation and are targets for cardiovascular diseases treatment. Here, the authors offer a structural basis for peptide recognition selectivity and activation of both endothelin receptors.

    • Yujie Ji
    • , Jia Duan
    •  & Yi Jiang

  • Article
    | Open Access

    The authors harness plasma focused ion beams for pseudo-atomic structure determination, reporting increased throughput and automation in in situ structural biology to elucidate structure-function relationships inside cells and tissues.

    • Casper Berger
    • , Maud Dumoux
    •  & Michael Grange

  • Article
    | Open Access

    The mode of cytokine receptor activation is diverse. Here, the authors find that the marine-sponge derived lectin ThC, a bivalent sugar binding protein, activates human cytokine receptor MPL. This mode of action resembles the pathogenic activation of MPL by mutant molecular chaperon calreticulin in hematologic malignancies.

    • Hiromi Watari
    • , Hiromu Kageyama
    •  & Ryuichi Sakai

  • Article
    | Open Access

    Previously, peptide selectivity in the VPAC receptor family of GPCRs was poorly understood. Here, authors combine cryo-EM and MD data to understand binding and selectivity of VPAC1R and PAC1R peptide agonists that can guide future drug development.

    • Sarah J. Piper
    • , Giuseppe Deganutti
    •  & Denise Wootten

  • Article
    | Open Access

    Here, the authors discover that ligandability of BTB domains correlates with the presence of μs-ms time scale dynamics. This finding suggests that protein dynamics may be a broadly applicable tool in drug discovery to assess the ligandability of novel and challenging targets.

    • Vladlena Kharchenko
    • , Brian M. Linhares
    •  & Łukasz Jaremko

  • Article
    | Open Access

    Retrieval of a new starting active compound with a novel scaffold during early drug development is an important but challenging task. Here, the authors propose a generative deep learning model and by applying this model they discover a potent and highly selective RIPK1 inhibitor with a previously unreported scaffold.

    • Yueshan Li
    • , Liting Zhang
    •  & Shengyong Yang

  • Article
    | Open Access

    Air-water interface and preferential orientation problems are crucial challenges in cryo-EM specimen preparation. Here, the authors utilize graphene-coated EM grids functionalized by salts with various electrostatic properties, successfully overcoming preferred orientation.

    • Ye Lu
    • , Nan Liu
    •  & Hong-Wei Wang

  • Article
    | Open Access

    Evidence suggests that fibrous aggregates of protein tau may be the proximal cause of Alzheimer’s disease. Here, using atomic structures of tau fibrils from brains of people with Alzheimer’s disease, the authors have found small-molecule drug leads that disaggregate tau fibrils in vitro.

    • Paul M. Seidler
    • , Kevin A. Murray
    •  & David S. Eisenberg

  • Article
    | Open Access

    High-resolution structures of mammalian prions have remained elusive. Here, Manka et al. report the cryo-EM structure of infectious RML prion fibrils from mice. Structural similarity with recently reported infectious 263K prion fibrils from hamsters now suggests a common prion architecture.

    • Szymon W. Manka
    • , Wenjuan Zhang
    •  & Jonathan D. F. Wadsworth

  • Article
    | Open Access

    Acetohydroxyacid synthase (AHAS) is the target of more than 50 commercial herbicides, with many site-of-action resistance isolates identified in weeds. Here, the authors report the structural and kinetic characterizations to explain the effect AHAS mutations have on herbicide potency.

    • Thierry Lonhienne
    • , Yan Cheng
    •  & Luke W. Guddat

  • Article
    | Open Access

    Here the authors describe the Waffle Method, aimed at increasing the throughput of and solves several challenges present in cryo-FIB/SEM sample preparation for cryo-ET analysis — the highest-resolution method for obtaining 3D views of native biological specimens in-situ.

    • Kotaro Kelley
    • , Ashleigh M. Raczkowski
    •  & Alex J. Noble

  • Article
    | Open Access

    The nonopioid sigma-1 receptor (σ1R) is localized to the endoplasmic reticulum (ER), interacts with multiple effector proteins and various synthetic ligands, and is implicated in many diseases. Here, authors provide structural and functional evidence to reveal the likely ligand entry pathway for σ1R.

    • Fuhui Meng
    • , Yang Xiao
    •  & Xiaoming Zhou

  • Article
    | Open Access

    The amphiphilic low-molecular-weight protein hydrophobin (HFBI) can self-assemble into a crystalline monolayer film. Here, the authors present a cryo-EM support film using such 2D crystals of hydrophobin HFBI and show that it protects specimen from the air-water interface and can help to overcome the preferred orientation problem of particles in cryo-EM.

    • Hongcheng Fan
    • , Bo Wang
    •  & Fei Sun

  • Article
    | Open Access

    Processing bodies are phase separated compartments enriched in translationally repressed mRNAs. Here, Smith et al. show that, in sensory neurons, eukaryotic elongation factor 2 kinase (eEF2K) plays key roles in the regulation of processing body abundance and the formation of translationally inactive ribosomes.

    • Patrick R. Smith
    • , Sarah Loerch
    •  & Zachary T. Campbell

  • Article
    | Open Access

    Here, the authors present a hierarchical disorder model for the analysis of disorder in both crystal and cryo-EM structures. They apply their approach to several structures of three proteins, including SARS-CoV-2 proteins, and discuss mechanistic and dynamical implications.

    • Nicholas M. Pearce
    •  & Piet Gros

  • Article
    | Open Access

    Micro-crystal electron diffraction (MicroED) has shown great potential for the structure determination of crystals that are too small for X-ray diffraction but MicroED sample preparation remains challenging. Here, the authors present Preassis, a pressure-assisted method for the preparation of MicroED specimens and demonstrate that Preassis can be applied to a wide range of protein crystal suspensions with low and high viscosities, as well as those with low crystal concentrations.

    • Jingjing Zhao
    • , Hongyi Xu
    •  & Xiaodong Zou

  • Article
    | Open Access

    Sequencing methods such as icSHAPE were developed to probe RNA structures transcriptome-wide in cells. To probe intact RNA structures, the authors develop icSHAPE-MaP and apply to Dicer-bound substrates showing that distance measuring is important for Dicer cleavage of pre-miRNAs.

    • Qing-Jun Luo
    • , Jinsong Zhang
    •  & Qiangfeng Cliff Zhang

  • Article
    | Open Access

    Adaptation of current algorithms to 3D SMLM data is currently problematic. Here the authors report a method that increases the signal-to-noise ratio and resolution of 3D single particle analysis in localization microscopy and enables determination of the symmetry groups of macromolecular complexes.

    • Hamidreza Heydarian
    • , Maarten Joosten
    •  & Bernd Rieger

  • Article
    | Open Access

    Tomographic reconstructions of cryopreserved specimens enable in-situ structural studies. Here, the authors present the beam image-shift electron cryo-tomography (BISECT) approach that accelerates data collection speed and improves the map resolution compared to earlier approaches and present the in vitro structure of a 300 kDa protein complex that was solved at 3.6 Å resolution as a test case.

    • Jonathan Bouvette
    • , Hsuan-Fu Liu
    •  & Alberto Bartesaghi

  • Article
    | Open Access

    Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.

    • Saminathan Ramakrishnan
    • , Jason R. Stagno
    •  & Yun-Xing Wang

  • Article
    | Open Access

    The viral Protein Kinase-1 (PK-1) phosphorylates the regulatory protein p6.9, which facilitates baculoviral genome release. Here, the authors combine X-ray crystallography with biophysical and biochemical analyses as well as molecular dynamics simulations to characterize Cydia pomenella granulovirus PK-1, which forms a dimer with a parallel side-to-side arrangement of the kinase domains and furthermore, they provide insights into its catalytic mechanism and evolutionary relationships with other kinases.

    • Michael R. Oliver
    • , Christopher R. Horne
    •  & James M. Murphy

  • Article
    | Open Access

    Accurately predicting the secondary structure of non-coding RNAs can help unravel their function. Here the authors propose a method integrating thermodynamic information and deep learning to improve the robustness of RNA secondary structure prediction compared to several existing algorithms.

    • Kengo Sato
    • , Manato Akiyama
    •  & Yasubumi Sakakibara

  • Article
    | Open Access

    Spy is an ATP independent chaperone that can act as both a holdase and a foldase towards topologically simple substrates. Assessing the interaction of Spy and apoflavodoxin, a complex client, the authors show that Spy’s activity is substrate specific. Spy binds partially unfolded states of apoflavodoxin tightly, which limits the possibility of folding and converts Spy to a pure holdase.

    • Rishav Mitra
    • , Varun V. Gadkari
    •  & James C. A. Bardwell

  • Article
    | Open Access

    Sorghum is a source of lignocellulosic biomass for the production of renewable fuels. Here the authors characterise the sorghum secondary cell wall using multi-dimensional magic angle spinning solid-state NMR and present a model dominated by interactions between three-fold screw xylan and amorphous cellulose.

    • Yu Gao
    • , Andrew S. Lipton
    •  & Jenny C. Mortimer

  • Article
    | Open Access

    The structure and dynamics of large proteins and complexes can be studied by methyl-NMR but resonance assignment is still challenging. Here, the authors present a NMR method that leverages optimal control pulse design to unambiguously distinguish between Leu and Val using a simple 2D HMQC experiment and they apply it to several proteins including Cas9, interleukin, and human translation initiation factor eIF4a.

    • Soumya P. Behera
    • , Abhinav Dubey
    •  & Haribabu Arthanari

  • Article
    | Open Access

    Due to the pulsed nature of X-ray free electron laser (XFEL) instruments the majority of protein crystals, which are injected using continuous jet injection techniques are wasted. Here, the authors present a microfluidic device to deliver aqueous protein crystal laden droplets segmented with an immiscible oil and demonstrate that with this device an approx. 60% reduction in sample waste was achieved for data collection of 3-deoxy-D-manno-octulosonate 8-phosphate synthase crystals at the EuXFEL.

    • Austin Echelmeier
    • , Jorvani Cruz Villarreal
    •  & Alexandra Ros

  • Article
    | Open Access

    Ribosome biogenesis in eukaryotes is a complex process that involves more than 200 protein factors. Here the authors present a structural analysis of a collection of human pre-60S structures sampled through a nuclear export adaptor NMD3, representing structural snapshots of pre-60S particles immediately before and after passing through nuclear pore complex.

    • Xiaomeng Liang
    • , Mei-Qing Zuo
    •  & Ning Gao

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