Structural biology articles within Nature Communications

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    | Open Access

    Dinoflagellates are ecologically important and essential to corals and other cnidarians as phytosymbionts, but their photosystems had been underexplored. Recently, photosystem I (PSI) of dinoflagellate Symbiodinium sp. was structurally characterized using cryo-Electron Microscopy (cryo-EM). These analyses revealed a distinct organization of the PSI supercomplex, including two previously unidentified subunits, PsaT and PsaU, and shed light on interactions between light harvesting antenna proteins and the PSI core. These results have implications with respect to the evolution of dinoflagellates and their association with cnidarians.

    • Senjie Lin
    • , Shuaishuai Wu
    •  & Arthur R. Grossman

  • Article
    | Open Access

    Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. Here the authors obtain crystal structures and NMR data to show the recognition of diaromatic peptide motifs on a noncanonical surface of the PEX13 SH3 domain, revealing a dynamic network which modulates peroxisomal matrix import.

    • Stefan Gaussmann
    • , Rebecca Peschel
    •  & Michael Sattler

  • Article
    | Open Access

    SV2A is a receptor for botulinum neurotoxin (BoNT) and new generation antiepileptic drugs (AEDs). Here the authors report cryo-EM structures of SV2A in complex with BoNT receptor binding domain and AEDs highlighting the difference in the binding affinity between AEDs.

    • Atsushi Yamagata
    • , Kaori Ito
    •  & Mikako Shirouzu

  • Article
    | Open Access

    Here, Schwartz, Bravo, and Ahsan et al. show how multi-subunit fusion proteins are arranged around a crRNA in a type III CRISPR-Cas effector to cleave target RNA. Structures and molecular dynamics of this complex show three distinct active sites that can be used for programmable RNA cleavage.

    • Evan A. Schwartz
    • , Jack P. K. Bravo
    •  & David W. Taylor

  • Article
    | Open Access

    The molecular heterogeneity of glycosylated biotherapeutics often complicates analysis by intact mass spectrometry. Here, the authors propose a simplified procedure for characterization that employs proton transfer charge reduction. Integration with glycomic and glycopeptide datasets can further provide glycoform-level information.

    • Luis F. Schachner
    • , Christopher Mullen
    •  & Wendy Sandoval

  • Article
    | Open Access

    Adenosine A3 receptor (A3AR) holds promise for treating inflammatory and cancer conditions. Here, Cai et al. present cryo-EM structures of  A3AR bound to agonists CF101 and CF102, offering insights into its activation and ligand interaction, crucial for developing targeted therapies.

    • Hongmin Cai
    • , Shimeng Guo
    •  & H. Eric Xu

  • Article
    | Open Access

    How RNA-binding proteins (RBPs) regulate gene expression via effectors of RNA processing is unclear. Here, the authors dissect the effector interface of an essential RBP, Unkempt, and investigate its contribution to translational control in cells.

    • Kriti Shah
    • , Shiyang He
    •  & Jernej Murn

  • Article
    | Open Access

    The structure and function of polymerase dimers of non-segmented, negative-strand RNA viruses are poorly understood. Here, this study presents the structural basis for dimerization of a paramyxovirus L–P polymerase and its role in genome replication.

    • Jin Xie
    • , Mohamed Ouizougun-Oubari
    •  & Shuai Chen

  • Article
    | Open Access

    The human Asc-1-4F2hc complex plays an important role in the neural development and stability. Here, authors determine the cryo-EM structures of Asc-1-4F2hc complex in three states, revealing its substrate recognition and transport mechanism.

    • Yaning Li
    • , Yingying Guo
    •  & Renhong Yan

  • Article
    | Open Access

    Asc1/CD98hc is a key regulator of small neutral amino acid transport in the brain and adipose tissue. Here, authors report the structure of semi-occluded hAsc1/CD98hc and provide a model for Asc1 exchange and facilitated diffusion modes of transport.

    • Josep Rullo-Tubau
    • , Maria Martinez-Molledo
    •  & Oscar Llorca

  • Article
    | Open Access

    Cystathionine beta-synthase is a conserved essential enzyme of one-carbon metabolism. Here, the authors show that the enzyme oligomerises to form filaments that undergo conformational and morphological changes in response to its activator S-adenosyl-L-methionine, the global methyl donor.

    • Thomas J. McCorvie
    • , Douglas Adamoski
    •  & Wyatt W. Yue

  • Article
    | Open Access

    CaV1.2 is crucial in cardiac, vascular and neuronal function, serving as a target for many drugs. Here, authors identify the binding site of herb-derived drug tetrandrine, and explore inhibitory mechanism of L/T-type selective DHP drug benidipine.

    • Yiqing Wei
    • , Zhuoya Yu
    •  & Yan Zhao

  • Article
    | Open Access

    Here, the authors structurally characterise the interaction between Acinetobacter phage AP205 and the type IV Acinetobacter pili using cryo-electron microscopy, uncovering the mechanistic determinants of this interaction.

    • Ran Meng
    • , Zhongliang Xing
    •  & Junjie Zhang

  • Article
    | Open Access

    It is hard to correlate force, torque and localization information. The authors report Combined Optical and Magnetic BIomolecule TWEEZers, COMBI-Tweez, that integrates optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy: they demonstrate visualisation of higher order structural motifs in DNA.

    • Jack W. Shepherd
    • , Sebastien Guilbaud
    •  & Mark C. Leake

  • Article
    | Open Access

    The accumulation of alpha-synuclein fibrils within neurons is the defining feature of Lewy body dementia (LBD). Here the authors report a method to produce large quantities of alpha-synuclein fibrils that reproduce the complex structure of the fibrils that accumulate in LBD brain tissue.

    • Dhruva D. Dhavale
    • , Alexander M. Barclay
    •  & Paul T. Kotzbauer

  • Article
    | Open Access

    Carbon monoxide dehydrogenases (CODH) employ artificial electron mediators like viologens for biocatalysis, but little is known about the interaction between the mediators and the enzyme. Here, the authors discover the critical site for viologen interactions at the D-cluster of Carboxydothermus hydrogenoformans CODH2 via alanine mutations and crystallography, and report variants with increased ethyl viologen affinity.

    • Suk Min Kim
    • , Sung Heuck Kang
    •  & Yong Hwan Kim

  • Article
    | Open Access

    Semaphorin 5A (Sema5A) forms complexes with heparan and chondroitin sulfate proteoglycans to regulate neuronal migration. Here, the authors show that the thrombospondin-like repeat 4 (TSR4) of Sema5A enables glycosaminoglycan association, multimerization, and neural progenitor cell distribution.

    • Gergely N. Nagy
    • , Xiao-Feng Zhao
    •  & E. Yvonne Jones

  • Article
    | Open Access

    High-resolution cryo-EM study of human muscle phosphorylase kinase reveals its complex structure and how calcium ions activate it, offering insights into glycogen metabolism and kinase regulation.

    • Xiaoke Yang
    • , Mingqi Zhu
    •  & Junyu Xiao

  • Article
    | Open Access

    The natural hallucinogen psilocybin — produced by so-called magic mushrooms — holds promise for the treatment of depression and other mental health conditions. Here, the authors provide a structural and biochemical analysis of the Psilocybe methyl transferase PsiM that provides mechanistic insight into the last step of psilocybin biosynthesis.

    • Jesse Hudspeth
    • , Kai Rogge
    •  & Sebastiaan Werten

  • Article
    | Open Access

    Photoreceptor proteins utilise biological chromophores to regulate a large range of cellular processes in response to light. Here the authors identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that not only utilise B12 but also contain biliverdin (BV) as an additional chromophore.

    • Shaowei Zhang
    • , Laura N. Jeffreys
    •  & Nigel S. Scrutton

  • Article
    | Open Access

    Designing a molecule that favorably binds to a protein pocket is a keystone of drug discovery. Zhung et al. devise DeepICL, which leverages the generalizable features of non-covalent protein-ligand interactions on a 3D molecular generative model, improving the quality of AI-designed molecules.

    • Wonho Zhung
    • , Hyeongwoo Kim
    •  & Woo Youn Kim

  • Article
    | Open Access

    The defense-associated sirtuin 2 (DSR2) effector protects bacteria from phage infection by depleting NAD+. Here, the authors employ biochemical and structural approaches to reveal the inhibition and activation mechanisms of DSR2 by the phage anti-DSR2 protein (DSAD1) and tail tube protein (TTP).

    • Hang Yin
    • , Xuzichao Li
    •  & Heng Zhang

  • Article
    | Open Access

    The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Here, authors present the high-resolution cryo-EM structure of its intact tail machine, and identify multiple hydrolytic and binding modules.

    • Rong-Cheng Yu
    • , Feng Yang
    •  & Cong-Zhao Zhou

  • Article
    | Open Access

    IGF2 has a distinct binding affinity for two insulin receptor (IR) isoforms and mimics insulin’s function. Here, the authors present the activation mechanism of IR by IGF2 and reveal the molecular basis for IGF2’s different affinity for two IR isoforms.

    • Weidong An
    • , Catherine Hall
    •  & Eunhee Choi

  • Article
    | Open Access

    The structure of the nucleosome-bound human Bre1 complex reveals that its two RING domains bind the acidic patch and nucleosomal DNA, directing the E2 enzyme and ubiquitin for H2BK120-specific ubiquitination. The binding mode suggests a possible regulatory mechanism through nucleosomal DNA flexibility.

    • Shuhei Onishi
    • , Kotone Uchiyama
    •  & Toru Sengoku

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