Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[17434]
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.
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Jun 2021
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Krios II-Titan Krios II at Diamond
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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
Diamond Proposal Number(s):
[14743]
Open Access
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.
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Jun 2021
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Krios I-Titan Krios I at Diamond
Krios II-Titan Krios II at Diamond
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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
Diamond Proposal Number(s):
[17171, 15422]
Open Access
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.
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Jun 2021
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I08-Scanning X-ray Microscopy beamline (SXM)
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James
Everett
,
Frederik
Lermyte
,
Jake
Brooks
,
Vindy
Tjendana-Tjhin
,
Germán
Plascencia-Villa
,
Ian
Hands-Portman
,
Jane M.
Donnelly
,
Kharmen
Billimoria
,
George
Perry
,
Xiongwei
Zhu
,
Peter J.
Sadler
,
Peter B.
O'Connor
,
Joanna F.
Collingwood
,
Neil D.
Telling
Diamond Proposal Number(s):
[15854]
Open Access
Abstract: The chemistry of copper and iron plays a critical role in normal brain function. A variety of enzymes and proteins containing positively charged Cu+, Cu2+, Fe2+, and Fe3+ control key processes, catalyzing oxidative metabolism and neurotransmitter and neuropeptide production. Here, we report the discovery of elemental (zero–oxidation state) metallic Cu0 accompanying ferromagnetic elemental Fe0 in the human brain. These nanoscale biometal deposits were identified within amyloid plaque cores isolated from Alzheimer’s disease subjects, using synchrotron x-ray spectromicroscopy. The surfaces of nanodeposits of metallic copper and iron are highly reactive, with distinctly different chemical and magnetic properties from their predominant oxide counterparts. The discovery of metals in their elemental form in the brain raises new questions regarding their generation and their role in neurochemistry, neurobiology, and the etiology of neurodegenerative disease.
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Jun 2021
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[24245]
Open Access
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.
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May 2021
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I08-Scanning X-ray Microscopy beamline (SXM)
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Giovanni
De Giudici
,
Carlo
Meneghini
,
Carla
Buosi
,
Ilaria
Carlomagno
,
Giuliana
Aquilanti
,
Tohru
Araki
,
Diana E.
Bedolla
,
Maria Antonietta
Casu
,
Antonietta
Cherchi
,
Alessandra
Gianoncelli
,
Antonella
Iadecola
,
Andrei C.
Kuncser
,
V. Adrian
Maraloiu
,
Olivier
Mathon
,
Valentina
Rimondi
,
Pierpaolo
Zuddas
,
Daniela
Medas
Diamond Proposal Number(s):
[16496]
Abstract: Biominerals are widespread in Nature and they precipitate to respond to different physiological purposes. A broad knowledge of their chemical and structural properties offers a unique opportunity to improve our capability to reconstruct actual and paleoenvironment. In this work, we show two case studies, bivalves and foraminifera grown in polluted sites that were characterized by applying different and complementary synchrotron radiation-based investigation techniques, mainly focused on the investigation of Zn incorporation in the biomineralized shells. Using scanning transmission X-ray microscopy (STXM) and X-ray micro-fluorescence (µ-XRF), we found the colocalization of elements across the shells, while we obtained information on chemical speciation of Zn by applying X-ray absorption spectroscopy (XAS). Noticeably, instead of metal dispersion in the Ca-carbonate shells, we found traces of several independent phases, in particular for Zn, dispersed generally as microscopic minerals. This work provides fundamental insight into the structural properties, coordinative and chemical environment of some marine biominerals. This new knowledge is fundamental to understand the biogeochemical processes and to develop effective environmental proxies.
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May 2021
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Krios III-Titan Krios III at Diamond
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Diamond Proposal Number(s):
[17434]
Open Access
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.
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May 2021
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B18-Core EXAFS
E01-JEM ARM 200CF
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Diamond Proposal Number(s):
[20856]
Open Access
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.
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May 2021
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Krios I-Titan Krios I at Diamond
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Open Access
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.
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May 2021
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[16952]
Open Access
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.
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May 2021
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