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88 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	Gating and modulation of a hetero-octameric AMPA glutamate receptor Danyang Zhang , Jake F. Watson , Peter M. Matthews , Ondrej Cais , Ingo H. Greger Nature 62 DOI: 10.1038/s41586-021-03613-0 Diamond Proposal Number(s): [17434] Show Abstract ▼ Abstract: AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties.	Jun 2021
Krios II-Titan Krios II at Diamond	3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme Melisa Lazaro , Roberto Melero , Charlotte Huet , Jorge Lopez-Alonso , Sandra Delgado , Alexandra Dodu , Eduardo M. Bruch , Luciano A. Abriata , Pedro M. Alzari , Mikel Valle , María-Natalia Lisa Communications Biology 4 DOI: 10.1038/s42003-021-02222-x Diamond Proposal Number(s): [14743] Open Access Show Abstract ▼ Abstract: Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs180) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs180 in bacterial physiology, the lack of structural data for these enzymes has limited the progress of functional studies. Here we show that the mycobacterial L-GDH180 (mL-GDH180) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH180 involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors for allosteric regulation. These findings uncover unique aspects of the structure-function relationship in the subfamily of L-GDHs.	Jun 2021
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond	A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit Andreas Schedlbauer , Idoia Iturrioz , Borja Ochoa-Lizarralde , Tammo Diercks , Jorge Pedro Lopez-Alonso , José Luis Lavin , Tatsuya Kaminishi , Retina Çapuni , Neha Dhimole , Elisa De Astigarraga , David Gil-Carton , Paola Fucini , Sean R. Connell Science Advances 7 DOI: 10.1126/sciadv.abf7547 Diamond Proposal Number(s): [17171, 15422] Open Access Show Abstract ▼ Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo–electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.	Jun 2021
E02-JEM ARM 300CF	Atomic diffusivities in amorphous and liquid Cu-Zr: Kirkendall effects and dependence on packing density S.v. Ketov , Yu P. Ivanov , B. Putz , Z. Zhang , J. Eckert , A. I. Greer Acta Materialia 33 DOI: 10.1016/j.actamat.2021.116993 Diamond Proposal Number(s): [24245] Open Access Show Abstract ▼ Abstract: A novel method for measurement of atomic interdiffusivity is applied to amorphous Cu-Zr close to its glass-transition temperature Tg. Sputter-deposited multilayers are examined in cross-section by transmission electron microscopy and energy-dispersive X-ray spectroscopy. Mapping the evolution of composition profiles gives the interdiffusivity, which is orders of magnitude higher than if coupled to the viscosity expected near Tg. Kirkendall drift of interlayer interfaces in both amorphous and supercooled liquid states (i.e. below and above Tg), and associated voiding in the liquid, show that the diffusivity of copper greatly exceeds that of zirconium. Amorphous Cu-Zr is known to show maxima in atomic packing density at sharply defined compositions. The comparison of the two compositions in the present work provides the first direct evidence that denser packing is associated with lower atomic interdiffusivity. The lower interdiffusivity is governed by a lower diffusivity of copper, and reflects a lessened degree of decoupling of the copper (fast) and zirconium (slow) diffusivities in an efficiently packed glass. The new insights help to understand issues ranging from glass-forming ability to the controlled generation of nanovoided structures.	May 2021
Krios III-Titan Krios III at Diamond	Structural basis of TRAPPIII‐mediated Rab1 activation Aaron M. N. Joiner , Ben P. Phillips , Kumar Yugandhar , Ethan J Sanford , Marcus B Smolka , Haiyuan Yu , Elizabeth A. Miller , J Christopher Fromme The Embo Journal 74 DOI: 10.15252/embj.2020107607 Diamond Proposal Number(s): [17434] Open Access Show Abstract ▼ Abstract: The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.	May 2021
B18-Core EXAFS E01-JEM ARM 200CF	Intercalating lithium into the lattice of silver nanoparticles boosts catalytic hydrogenation of carbon–oxygen bonds Xin-Ping Duan , Tianyi Chen , Tianxiang Chen , Lele Huang , Li Ye , Benedict T. W. Lo , Youzhu Yuan , Shik Chi Edman Tsang Chemical Science 8 DOI: 10.1039/D1SC01700D Diamond Proposal Number(s): [20856] Open Access Show Abstract ▼ Abstract: Coinage metal nanoparticles with high dispersion can serve as highly efficient heterogeneous catalysts. However, owing to their low melting point, poor thermal stability remains a major obstacle towards their application under reaction conditions. It is a common practice to use porous inorganic templates such as mesoporous silica SBA-15 to disperse Ag nanoparticles (NPs) against aggregation but their stability is far from satisfactory. Here, we show that the catalytic activity for hydrogenation of dimethyl oxalate (DMO) to methyl glycolate (MG) over Ag NPs dispersed on SBA-15 silica can be further promoted by incorporation of alkali metal ions at small loading, which follows the inverse order of their cationic size: Li+ > Na+ > K+ > Rb+. Among these, 5Ag1–Li0.05/SBA-15 can double the MG yield compared to pristine 5Ag/SBA-15 under identical conditions with superior thermal stability. Akin to the effect of an ionic surfactant on stabilization of a micro-emulsion, the cationic charge of an alkali metal ion can maintain dispersion and modulate the surface valence of Ag NPs. Interstitial Li in the octahedral holes of the face center packed Ag lattice is for the first time confirmed by X-ray pair distribution function and electron ptychography. It is believed that this interstitial-stabilization of coinage metal nanoparticles could be broadly applicable to multi-metallic nanomaterials for a broad range of C–O bond activating catalytic reactions of esters.	May 2021
Krios I-Titan Krios I at Diamond	Cryo-EM studies of Phosphatidylinositol-3-kinase related kinase (PIKK) structures from yeast: Transcription-associated protein 1 (Tra1) and Mitosis-entry checkpoint 1 (Mec1), and their role as conserved genomic regulators Luis Miguel Diaz-Santin Open Access Show Abstract ▼ Abstract: The regulation of the genome is an essential biological task. In eukaryotes, fundamental nuclear processes such as DNA replication, transcription and repair require a large variety of protein effectors to ensure the correct transmission of genetic information, for regulated gene expression and to maintain genome integrity. The phosphatidylinositol 3-kinase-related kinase (PIKK) protein family represents a group of very large and highly conserved Ser/Thr-protein kinases, where most function in genome regulation processes. S. cerevisiae proteins Tra1 and Mec1 (known as TRRAP and ATR in humans) are two essential PIKKs found in the nucleus. Tra1 is a 3,744-residue protein and a shared subunit between the chromatin modifying complexes SAGA and NuA4. Tra1 stimulates transcriptional activation by directly interacting with transcription activators and is also involved in DNA repair. Here, I present the near-atomic resolution cryo-EM structure of the full-length Tra1 polypeptide. A “de novo” atomic model was built from the map, revealing the unique arrangement of Tra1 alpha-solenoid, which is organised into an N-terminal Finger segment inserted into a circular Cradle region before the Kinase domain. Structural interpretation of previously published Tra1 mutants allowed to identify a Gal4 binding region. Mec1 is a 2,368-residue protein that forms a complex with Ddc2 (ATRIP in humans), and participates in the DNA-Damage-Response, Replication-Stress-Response, in telomere maintenance and meiosis, and its kinase activity influences cell cycle progression. Here, I present the high-resolution cryo-EM structure of the heterodimeric Mec1-Ddc2 complex, providing the first complete atomic model of Mec1. The structure reveals how the complex is assembled, showing extensive interactions between Ddc2 solenoid region and Mec1. The map also shows the integration point of Ddc2 N-terminal region into the complex, and together with existing structural data for the interaction of Ddc2 coiled-coil with RPA, an integrative model shed light in the understanding of Mec1 recruitment to RPA-coated ssDNA.	May 2021
E02-JEM ARM 300CF	Atomic resolution HOLZ-STEM imaging of atom position modulation in oxide heterostructures Magnus Nord , Juri Barthel , Christopher S. Allen , Damien Mcgrouther , Angus I. Kirkland , Ian Maclaren Ultramicroscopy 168 DOI: 10.1016/j.ultramic.2021.113296 Diamond Proposal Number(s): [16952] Open Access Show Abstract ▼ Abstract: It is shown that higher order Laue zone (HOLZ) rings in high energy electron diffraction are specific to individual columns of atoms, and show different strengths, structure and radii for different atom columns along the same projection in a structure. An atomic resolution 4-dimensional STEM dataset is recorded from a <110> direction in a perovskite trilayer, where only the central LaFeO3 layer should show a period doubling that gives rise to an extra HOLZ ring. Careful comparison between experiment and multislice simulations is used to understand the origins of all features in the patterns. A strong HOLZ ring is seen for the La-O columns, indicating strong La position modulation along this direction, whereas a weaker ring is seen along the O columns, and a very weak ring is seen along the Fe columns. This demonstrates that atomic resolution HOLZ-STEM is a feasible method for investigating the 3D periodicity of crystalline materials with atomic resolution.	May 2021
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond Krios III-Titan Krios III at Diamond Krios IV-Titan Krios IV at Diamond Talos-Talos Arctica at Diamond	Single particle cryo-electron microscopy: From sample to structure Joshua B. R. White , Daniel P. Maskell , Andrew Howe , Martin Harrow , Daniel K. Clare , C. Alistair Siebert , Emma L. Hesketh , Rebecca F. Thompson Journal Of Visualized Experiments DOI: 10.3791/62415 Diamond Proposal Number(s): [23047] Open Access Show Abstract ▼ Abstract: Cryo-electron microscopy (cryoEM) is a powerful technique for structure determination of macromolecular complexes, via single particle analysis (SPA). The overall process involves i) vitrifying the specimen in a thin film supported on a cryoEM grid; ii) screening the specimen to assess particle distribution and ice quality; iii) if the grid is suitable, collecting a single particle dataset for analysis; and iv) image processing to yield an EM density map. In this protocol, an overview for each of these steps is provided, with a focus on the variables which a user can modify during the workflow and the troubleshooting of common issues. With remote microscope operation becoming standard in many facilities, variations on imaging protocols to assist users in efficient operation and imaging when physical access to the microscope is limited will be described.	May 2021
Krios II-Titan Krios II at Diamond	Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine Yasunori Watanabe , Luiza Mendonca , Elizabeth R. Allen , Andrew Howe , Mercede Lee , Joel D. Allen , Himanshi Chawla , David Pulido , Francesca Donnellan , Hannah Davies , Marta Ulaszewska , Sandra Belij-Rammerstorfer , Susan Morris , Anna-Sophia Krebs , Wanwisa Dejnirattisai , Juthathip Mongkolsapaya , Piyada Supasa , Gavin R. Screaton , Catherine M. Green , Teresa Lambe , Peijun Zhang , Sarah C. Gilbert , Max Crispin Acs Central Science DOI: 10.1021/acscentsci.1c00080 Diamond Proposal Number(s): [18477, 21005, 21004] Show Abstract ▼ Abstract: Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation, and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirm the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.	Apr 2021

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