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286 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
	Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10 Yuguang Zhao , Daming Zhou , Tao Ni , Dimple Karia , Abhay Kotecha , Xiangxi Wang , Zihe Rao , E. Yvonne Jones , Elizabeth E. Fry , Jingshan Ren , David I. Stuart Nature Communications 11 DOI: 10.1038/s41467-019-13936-2 Open Access Show Abstract ▼ Abstract: Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry receptor for the largest receptor-group of hand-foot-and-mouth disease causing viruses, which includes CV-A10. We report here structures of CV-A10 mature virus alone and in complex with KRM1 as well as of the CV-A10 A-particle. The receptor spans the viral canyon with a large footprint on the virus surface. The footprint has some overlap with that seen for the neonatal Fc receptor complexed with enterovirus E6 but is larger and distinct from that of another enterovirus receptor SCARB2. Reduced occupancy of a particle-stabilising pocket factor in the complexed virus and the presence of both unbound and expanded virus particles suggests receptor binding initiates a cascade of conformational changes that produces expanded particles primed for viral uncoating.	Jan 2020
I24-Microfocus Macromolecular Crystallography	Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin Samir Olatunji , Xiaoxiao Yu , Jonathan Bailey , Chia-ying Huang , Marta Zapotoczna , Katherine Bowen , Maja Remškar , Rolf Müller , Eoin M. Scanlan , Joan A. Geoghegan , Vincent Olieric , Martin Caffrey Nature Communications 11 DOI: 10.1038/s41467-019-13724-y Diamond Proposal Number(s): [17810] Open Access Show Abstract ▼ Abstract: Antimicrobial resistance is a major global threat that calls for new antibiotics. Globomycin and myxovirescin are two natural antibiotics that target the lipoprotein-processing enzyme, LspA, thereby compromising the integrity of the bacterial cell envelope. As part of a project aimed at understanding their mechanism of action and for drug development, we provide high-resolution crystal structures of the enzyme from the human pathogen methicillin-resistant Staphylococcus aureus (MRSA) complexed with globomycin and with myxovirescin. Our results reveal an instance of convergent evolution. The two antibiotics possess different molecular structures. Yet, they appear to inhibit identically as non-cleavable tetrahedral intermediate analogs. Remarkably, the two antibiotics superpose along nineteen contiguous atoms that interact similarly with LspA. This 19-atom motif recapitulates a part of the substrate lipoprotein in its proposed binding mode. Incorporating this motif into a scaffold with suitable pharmacokinetic properties should enable the development of effective antibiotics with built-in resistance hardiness.	Jan 2020
B21-High Throughput SAXS	Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Doo Nam Kim , Bernhard C. Thiel , Tyler Mrozowich , Scott P. Hennelly , Ivo L. Hofacker , Trushar R. Patel , Karissa Y. Sanbonmatsu Nature Communications 11 DOI: 10.1038/s41467-019-13942-4 Diamond Proposal Number(s): [16028] Open Access Show Abstract ▼ Abstract: Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.	Jan 2020
I11-High Resolution Powder Diffraction	Hydroxyl-rich macromolecules enable the bio-inspired synthesis of single crystal nanocomposites Yi-yeoun Kim , Robert Darkins , Alexander Broad , Alexander N. Kulak , Mark A. Holden , Ouassef Nahi , Steven P. Armes , Chiu C. Tang , Rebecca F. Thompson , Frederic Marin , Dorothy M. Duffy , Fiona C. Meldrum Nature Communications 10 DOI: 10.1038/s41467-019-13422-9 Open Access Show Abstract ▼ Abstract: Acidic macromolecules are traditionally considered key to calcium carbonate biomineralisation and have long been first choice in the bio-inspired synthesis of crystalline materials. Here, we challenge this view and demonstrate that low-charge macromolecules can vastly outperform their acidic counterparts in the synthesis of nanocomposites. Using gold nanoparticles functionalised with low charge, hydroxyl-rich proteins and homopolymers as growth additives, we show that extremely high concentrations of nanoparticles can be incorporated within calcite single crystals, while maintaining the continuity of the lattice and the original rhombohedral morphologies of the crystals. The nanoparticles are perfectly dispersed within the host crystal and at high concentrations are so closely apposed that they exhibit plasmon coupling and induce an unexpected contraction of the crystal lattice. The versatility of this strategy is then demonstrated by extension to alternative host crystals. This simple and scalable occlusion approach opens the door to a novel class of single crystal nanocomposites.	Dec 2019
I16-Materials and Magnetism	Observation of strong nonlinear interactions in parametric down-conversion of X-rays into ultraviolet radiation S. Sofer , O. Sefi , E. Strizhevsky , H. Aknin , S. P. Collins , G. Nisbet , B. Detlefs , Ch. J. Sahle , S. Shwartz Nature Communications 10 DOI: 10.1038/s41467-019-13629-w Diamond Proposal Number(s): [17527, 22041] Open Access Show Abstract ▼ Abstract: Nonlinear interactions between X-rays and long wavelength radiation can be used as a powerful atomic-scale probe for light-matter interactions and for properties of valence electrons. However, reported X-ray nonlinear effects were small and their observations required tremendous efforts. Here we report the observation of strong nonlinearities in parametric down-conversion (PDC) of X-rays to long wavelength radiation in gallium arsenide and lithium niobate crystals, with efficiencies about 4 orders of magnitude stronger than the efficiencies measured in any material studied before. Furthermore, we show that the efficiency in the ferroelectric phase of strontium barium niobite is two orders of magnitude stronger than in its paraelectric phase. This observation suggests that the lack of inversion symmetry is the origin for the strong observed nonlinearity. Additionally, we demonstrate the ability to use the effect for the investigation of the spectral response of non-centrosymmetric materials at wavelengths ranging from infrared to soft X-rays.	Dec 2019
I07-Surface & interface diffraction	Controlling energy levels and Fermi level en route to fully tailored energetics in organic semiconductors Ross Warren , Alberto Privitera , Pascal Kaienburg , Andreas E. Lauritzen , Oliver Thimm , Jenny Nelson , Moritz K. Riede Nature Communications 10 DOI: 10.1038/s41467-019-13563-x Diamond Proposal Number(s): [20426] Open Access Show Abstract ▼ Abstract: Simultaneous control over both the energy levels and Fermi level, a key breakthrough for inorganic electronics, has yet to be shown for organic semiconductors. Here, energy level tuning and molecular doping are combined to demonstrate controlled shifts in ionisation potential and Fermi level of an organic thin film. This is achieved by p-doping a blend of two host molecules, zinc phthalocyanine and its eight-times fluorinated derivative, with tunable energy levels based on mixing ratio. The doping efficiency is found to depend on host mixing ratio, which is explained using a statistical model that includes both shifts of the host’s ionisation potentials and, importantly, the electron affinity of the dopant. Therefore, the energy level tuning effect has a crucial impact on the molecular doping process. The practice of comparing host and dopant energy levels must consider the long-range electrostatic shifts to consistently explain the doping mechanism in organic semiconductors.	Dec 2019
I11-High Resolution Powder Diffraction	Single phase charge ordered stoichiometric CaFe3O5 with commensurate and incommensurate trimeron ordering Simon J. Cassidy , Fabio Orlandi , Pascal Manuel , Simon J. Clarke Nature Communications 10 DOI: 10.1038/s41467-019-13450-5 Diamond Proposal Number(s): [13284, 18786] Open Access Show Abstract ▼ Abstract: Mixed-valent transition metal compounds display complex structural, electronic and magnetic properties which can often be exquisitely tuned. Here the charge-ordered state of stoichiometric CaFe3O5 is probed using neutron powder diffraction, Monte Carlo simulation and symmetry analysis. Magnetic ordering is dominated by the formation of ferromagnetic Fe3+–Fe2+–Fe3+ trimers which are evident above the magnetic ordering transition. Between TN = 289 K and 281 K an incommensurate magnetically ordered phase develops due to magnetic frustration, but a spin Jahn-Teller distortion lifts the frustration and enables the magnetic ordering to lock in to a charge-ordered commensurate state at lower temperatures. Stoichiometric CaFe3O5 exhibits single phase behaviour throughout and avoids the phase separation into two distinct crystallographic phases with different magnetic structures and Fe valence distributions reported recently, which likely occurs due to partial Fe2+ for Ca2+ substitution. This underlines the sensitivity of the magnetism and chemistry of these mixed-valent systems to composition.	Dec 2019
I10-Beamline for Advanced Dichroism	Temperature dependence of spherical electron transfer in a nanosized [Fe14] complex Wei Huang , Shuqi Wu , Xiangwei Gu , Yao Li , Atsushi Okazawa , Norimichi Kojima , Shinya Hayami , Michael L. Baker , Peter Bencok , Mariko Noguchi , Yuji Miyazaki , Motohiro Nakano , Takumi Nakanishi , Shinji Kanegawa , Yuji Inagaki , Tatsuya Kawae , Gui-lin Zhuang , Yoshihito Shiota , Kazunari Yoshizawa , Dayu Wu , Osamu Sato Nature Communications 10 DOI: 10.1038/s41467-019-13279-y Diamond Proposal Number(s): [17723] Open Access Show Abstract ▼ Abstract: The study of transition metal clusters exhibiting fast electron hopping or delocalization remains challenging, because intermetallic communications mediated through bridging ligands are normally weak. Herein, we report the synthesis of a nanosized complex, [Fe(Tp)(CN)3]8[Fe(H2O)(DMSO)]6 (abbreviated as [Fe14], Tp−, hydrotris(pyrazolyl)borate; DMSO, dimethyl sulfoxide), which has a fluctuating valence due to two mobile d-electrons in its atomic layer shell. The rate of electron transfer of [Fe14] complex demonstrates the Arrhenius-type temperature dependence in the nanosized spheric surface, wherein high-spin centers are ferromagnetically coupled, producing an S = 14 ground state. The electron-hopping rate at room temperature is faster than the time scale of Mössbauer measurements (<~10−8 s). Partial reduction of N-terminal high spin FeIII sites and electron mediation ability of CN ligands lead to the observation of both an extensive electron transfer and magnetic coupling properties in a precisely atomic layered shell structure of a nanosized [Fe14] complex.	Dec 2019
Krios I-Titan Krios I at Diamond	Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone Carol Cho , Juwon Jang , Yujin Kang , Hiroki Watanabe , Takayuki Uchihashi , Seung Joong Kim , Koichi Kato , Ja Yil Lee , Ji-joon Song Nature Communications 10 DOI: 10.1038/s41467-019-13743-9 Diamond Proposal Number(s): [22985] Open Access Show Abstract ▼ Abstract: The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate nucleosome density and chromatin dynamics. Here, we demonstrate that the fission yeast ATAD2 homolog, Abo1, deposits histone H3–H4 onto DNA in an ATP-hydrolysis-dependent manner by in vitro reconstitution and single-tethered DNA curtain assays. We present cryo-EM structures of an ATAD2 family ATPase to atomic resolution in three different nucleotide states, revealing unique structural features required for histone loading on DNA, and directly visualize the transitions of Abo1 from an asymmetric spiral (ATP-state) to a symmetric ring (ADP- and apo-states) using high-speed atomic force microscopy (HS-AFM). Furthermore, we find that the acidic pore of ATP-Abo1 binds a peptide substrate which is suggestive of a histone tail. Based on these results, we propose a model whereby Abo1 facilitates H3–H4 loading by utilizing ATP.	Dec 2019
I03-Macromolecular Crystallography	Structural basis for Fullerene geometry in a human endogenous retrovirus capsid Oliver Acton , Tim Grant , Giuseppe Nicastro , Neil J. Ball , David C. Goldstone , Laura E. Robertson , Kasim Sader , Andrea Nans , Andres Ramos , Jonathan P. Stoye , Ian A. Taylor , Peter B. Rosenthal Nature Communications 10 DOI: 10.1038/s41467-019-13786-y Diamond Proposal Number(s): [13775] Open Access Show Abstract ▼ Abstract: The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.	Dec 2019

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