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564 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
Krios I-Titan Krios I at Diamond	Structural atlas of a human gut crassvirus Oliver W. Bayfield , Andrey N. Shkoporov , Natalya Yutin , Ekaterina V. Khokhlova , Jake L. R. Smith , Dorothy E. D. P. Hawkins , Eugene V. Koonin , Colin Hill , Alfred A. Antson Nature 25 DOI: 10.1038/s41586-023-06019-2 Diamond Proposal Number(s): [19832] Open Access Show Abstract ▼ Abstract: CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses4,5. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss0016, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the ‘crass fold’, that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.	May 2023
Krios IV-Titan Krios IV at Diamond	Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex Mandy S. M. Wan , Reyhan Muhammad , Marios G. Koliopoulos , Theodoros I. Roumeliotis , Jyoti S. Choudhary , Claudio Alfieri Nature Communications 14 DOI: 10.1038/s41467-023-38276-0 Diamond Proposal Number(s): [21809] Open Access Show Abstract ▼ Abstract: Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.	May 2023
I06-Nanoscience	Antiferromagnetic half-skyrmions electrically generated and controlled at room temperature O. J. Amin , S. F. Poole , S. Reimers , L. X. Barton , A. Dal Din , F. Maccherozzi , S. S. Dhesi , V. Novák , F. Krizek , J. S. Chauhan , R. P. Campion , A. W. Rushforth , T. Jungwirth , O. A. Tretiakov , K. W. Edmonds , P. Wadley Nature Nanotechnology 6 DOI: 10.1038/s41565-023-01386-3 Diamond Proposal Number(s): [26255, 27845] Open Access Show Abstract ▼ Abstract: Topologically protected magnetic textures are promising candidates for information carriers in future memory devices, as they can be efficiently propelled at very high velocities using current-induced spin torques. These textures—nanoscale whirls in the magnetic order—include skyrmions, half-skyrmions (merons) and their antiparticles. Antiferromagnets have been shown to host versions of these textures that have high potential for terahertz dynamics, deflection-free motion and improved size scaling due to the absence of stray field. Here we show that topological spin textures, merons and antimerons, can be generated at room temperature and reversibly moved using electrical pulses in thin-film CuMnAs, a semimetallic antiferromagnet that is a testbed system for spintronic applications. The merons and antimerons are localized on 180° domain walls, and move in the direction of the current pulses. The electrical generation and manipulation of antiferromagnetic merons is a crucial step towards realizing the full potential of antiferromagnetic thin films as active components in high-density, high-speed magnetic memory devices.	May 2023
E02-JEM ARM 300CF	Mapping nanocrystalline disorder within an amorphous metal–organic framework Adam F. Sapnik , Chao Sun , Joonatan E. M. Laulainen , Duncan N. Johnstone , Rik Brydson , Timothy Johnson , Paul A. Midgley , Thomas D. Bennett , Sean M. Collins Communications Chemistry 6 DOI: 10.1038/s42004-023-00891-9 Diamond Proposal Number(s): [20198] Open Access Show Abstract ▼ Abstract: Intentionally disordered metal–organic frameworks (MOFs) display rich functional behaviour. However, the characterisation of their atomic structures remains incredibly challenging. X-ray pair distribution function techniques have been pivotal in determining their average local structure but are largely insensitive to spatial variations in the structure. Fe-BTC (BTC = 1,3,5-benzenetricarboxylate) is a nanocomposite MOF, known for its catalytic properties, comprising crystalline nanoparticles and an amorphous matrix. Here, we use scanning electron diffraction to first map the crystalline and amorphous components to evaluate domain size and then to carry out electron pair distribution function analysis to probe the spatially separated atomic structure of the amorphous matrix. Further Bragg scattering analysis reveals systematic orientational disorder within Fe-BTC’s nanocrystallites, showing over 10° of continuous lattice rotation across single particles. Finally, we identify candidate unit cells for the crystalline component. These independent structural analyses quantify disorder in Fe-BTC at the critical length scale for engineering composite MOF materials.	May 2023
B18-Core EXAFS E01-JEM ARM 200CF	Isolated PdO sites on SiO2-supported NiO nanoparticles as active sites for allylic alcohol selective oxidation Aleksandra Ziarko , Thomas J. A. Slater , Mark A. Isaacs , Lee J. Durndell , Christopher M. A. Parlett Catalysis Science & Technology 40 DOI: 10.1039/D3CY00198A Diamond Proposal Number(s): [21795, 15151] Open Access Show Abstract ▼ Abstract: Catalytic allylic alcohol oxidation to aldehydes is an industrial process that necessitates chemoselectivity. Surface PdO (on Pd) enables this transformation but does not represent optimal metal utilisation. Here we report a facile synthesis route to produce isolated surface PdO catalytic sites on an earth-abundant metal (NiO) for cinnamyl alcohol oxidation.	May 2023
Krios V-Titan Krios V at Diamond	Signal peptide mimicry primes Sec61 for client-selective inhibition Shahid Rehan , Dale Tranter , Phillip P. Sharp , Gregory B. Craven , Eric Lowe , Janet L. Anderl , Tony Muchamuel , Vahid Abrishami , Suvi Kuivanen , Nicole A. Wenzell , Andy Jennings , Chakrapani Kalyanaraman , Tomas Strandin , Matti Javanainen , Olli Vapalahti , Matthew P. Jacobson , Dustin Mcminn , Christopher J. Kirk , Juha T. Huiskonen , Jack Taunton , Ville O. Paavilainen Nature Chemical Biology 1808 DOI: 10.1038/s41589-023-01326-1 Open Access Show Abstract ▼ Abstract: Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.	May 2023
Krios II-Titan Krios II at Diamond	Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly Rebecca Conners , Rayén Ignacia León-Quezada , Mathew Mclaren , Nicholas J. Bennett , Bertram Daum , Jasna Rakonjac , Vicki Gold Nature Communications 14 DOI: 10.1038/s41467-023-37915-w Diamond Proposal Number(s): [25452] Open Access Show Abstract ▼ Abstract: Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.	May 2023
Krios IV-Titan Krios IV at Diamond	mRNA recognition and packaging by the human transcription–export complex Belén Pacheco-Fiallos , Matthias K. Vorleander , Daria Riabov-Bassat , Laura Fin , Francis J. O'Reilly , Farja I. Ayala , Ulla Schellhaas , Juri Rappsilber , Clemens Plaschka Nature 8 DOI: 10.1038/s41586-023-05904-0 Show Abstract ▼ Abstract: Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription–export complex (TREX) for nuclear export1,2. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood3. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.	Apr 2023
I06-Nanoscience	Current-driven writing process in antiferromagnetic Mn2Au for memory applications S. Reimers , Y. Lytvynenko , Y. R. Niu , E. Golias , B. Sarpi , L. S. I. Veiga , T. Denneulin , A. Kovács , R. E. Dunin-Borkowski , J. Bläßer , M. Klaui , M. Jourdan Nature Communications 14 DOI: 10.1038/s41467-023-37569-8 Diamond Proposal Number(s): [30141] Open Access Show Abstract ▼ Abstract: Current pulse driven Néel vector rotation in metallic antiferromagnets is one of the most promising concepts in antiferromagnetic spintronics. We show microscopically that the Néel vector of epitaxial thin films of the prototypical compound Mn2Au can be reoriented reversibly in the complete area of cross shaped device structures using single current pulses. The resulting domain pattern with aligned staggered magnetization is long term stable enabling memory applications. We achieve this switching with low heating of ≈20 K, which is promising regarding fast and efficient devices without the need for thermal activation. Current polarity dependent reversible domain wall motion demonstrates a Néel spin-orbit torque acting on the domain walls.	Apr 2023
B16-Test Beamline DIAD-Dual Imaging and Diffraction Beamline E01-JEM ARM 200CF E02-JEM ARM 300CF I08-Scanning X-ray Microscopy beamline (SXM) I12-JEEP: Joint Engineering, Environmental and Processing I13-1-Coherence I13-2-Diamond Manchester Imaging I14-Hard X-ray Nanoprobe	Synchrotron X-ray studies of the structural and functional hierarchies in mineralised human dental enamel: a state-of-the-art review Cyril Besnard , Ali Marie , Sisini Sasidharan , Robert A. Harper , Richard M. Shelton , Gabriel Landini , Alexander M. Korsunsky Dentistry Journal 11 DOI: 10.3390/dj11040098 Open Access Show Abstract ▼ Abstract: Hard dental tissues possess a complex hierarchical structure that is particularly evident in enamel, the most mineralised substance in the human body. Its complex and interlinked organisation at the Ångstrom (crystal lattice), nano-, micro-, and macro-scales is the result of evolutionary optimisation for mechanical and functional performance: hardness and stiffness, fracture toughness, thermal, and chemical resistance. Understanding the physical–chemical–structural relationships at each scale requires the application of appropriately sensitive and resolving probes. Synchrotron X-ray techniques offer the possibility to progress significantly beyond the capabilities of conventional laboratory instruments, i.e., X-ray diffractometers, and electron and atomic force microscopes. The last few decades have witnessed the accumulation of results obtained from X-ray scattering (diffraction), spectroscopy (including polarisation analysis), and imaging (including ptychography and tomography). The current article presents a multi-disciplinary review of nearly 40 years of discoveries and advancements, primarily pertaining to the study of enamel and its demineralisation (caries), but also linked to the investigations of other mineralised tissues such as dentine, bone, etc. The modelling approaches informed by these observations are also overviewed. The strategic aim of the present review was to identify and evaluate prospective avenues for analysing dental tissues and developing treatments and prophylaxis for improved dental health.	Apr 2023

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