I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[16258]
Open Access
Abstract: Cross-talk between ubiquitination and ADP-ribosylation regulates spatiotemporal recruitment of key players in many signaling pathways. The DELTEX family ubiquitin ligases (DTX1 to DTX4 and DTX3L) are characterized by a RING domain followed by a C-terminal domain (DTC) of hitherto unknown function. Here, we use two label-free mass spectrometry techniques to investigate the interactome and ubiquitinated substrates of human DTX2 and identify a large proportion of proteins associated with the DNA damage repair pathway. We show that DTX2-catalyzed ubiquitination of these interacting proteins requires PARP1/2-mediated ADP-ribosylation and depends on the DTC domain. Using a combination of structural, biochemical, and cell-based techniques, we show that the DTX2 DTC domain harbors an ADP-ribose–binding pocket and recruits poly-ADP-ribose (PAR)–modified proteins for ubiquitination. This PAR-binding property of DTC domain is conserved across the DELTEX family E3s. These findings uncover a new ADP-ribose–binding domain that facilitates PAR-dependent ubiquitination.
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Aug 2020
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[18598]
Open Access
Abstract: Toxin-antitoxin systems are widespread stress-responsive elements, many of whose functions remain largely unknown. Here, we characterize the four DUF1814-family nucleotidyltransferase-like toxins (MenT1–4) encoded by the human pathogen Mycobacterium tuberculosis. Toxin MenT3 inhibited growth of M. tuberculosis when not antagonized by its cognate antitoxin, MenA3. We solved the structures of toxins MenT3 and MenT4 to 1.6 and 1.2 Å resolution, respectively, and identified the biochemical activity and target of MenT3. MenT3 blocked in vitro protein expression and prevented tRNA charging in vivo. MenT3 added pyrimidines (C or U) to the 3′-CCA acceptor stems of uncharged tRNAs and exhibited strong substrate specificity in vitro, preferentially targeting tRNASer from among the 45 M. tuberculosis tRNAs. Our study identifies a previously unknown mechanism that expands the range of enzymatic activities used by bacterial toxins, uncovering a new way to block protein synthesis and potentially treat tuberculosis and other infections.
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Jul 2020
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I05-ARPES
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Shuo-ying
Yang
,
Yaojia
Wang
,
Brenden R.
Ortiz
,
Defa
Liu
,
Jacob
Gayles
,
Elena
Derunova
,
Rafael
Gonzalez-hernandez
,
Libor
Šmejkal
,
Yulin
Chen
,
Stuart S. P.
Parkin
,
Stephen D.
Wilson
,
Eric S.
Toberer
,
Tyrel
Mcqueen
,
Mazhar N.
Ali
Diamond Proposal Number(s):
[22367]
Open Access
Abstract: The anomalous Hall effect (AHE) is one of the most fundamental phenomena in physics. In the highly conductive regime, ferromagnetic metals have been the focus of past research. Here, we report a giant extrinsic AHE in KV3Sb5, an exfoliable, highly conductive semimetal with Dirac quasiparticles and a vanadium Kagome net. Even without report of long range magnetic order, the anomalous Hall conductivity reaches 15,507 Ω−1 cm−1 with an anomalous Hall ratio of ≈ 1.8%; an order of magnitude larger than Fe. Defying theoretical expectations, KV3Sb5 shows enhanced skew scattering that scales quadratically, not linearly, with the longitudinal conductivity, possibly arising from the combination of highly conductive Dirac quasiparticles with a frustrated magnetic sublattice. This allows the possibility of reaching an anomalous Hall angle of 90° in metals. This observation raises fundamental questions about AHEs and opens new frontiers for AHE and spin Hall effect exploration, particularly in metallic frustrated magnets.
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Jul 2020
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I18-Microfocus Spectroscopy
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M.
Bourdenx
,
A.
Nioche
,
S.
Dovero
,
M.-l.
Arotcarena
,
S.
Camus
,
G.
Porras
,
M.-l.
Thiolat
,
N. P.
Rougier
,
A.
Prigent
,
P.
Aubert
,
S.
Bohic
,
C.
Sandt
,
F.
Laferrière
,
E.
Doudnikoff
,
N.
Kruse
,
B.
Mollenhauer
,
S.
Novello
,
M.
Morari
,
T.
Leste-lasserre
,
I. Trigo
Damas
,
M.
Goillandeau
,
C.
Perier
,
C.
Estrada
,
N.
Garcia-carrillo
,
A.
Recasens
,
N. N.
Vaikath
,
O. M. A.
El-agnaf
,
M. T.
Herrero
,
P.
Derkinderen
,
M.
Vila
,
J. A.
Obeso
,
B.
Dehay
,
E.
Bezard
Diamond Proposal Number(s):
[13009]
Open Access
Abstract: Dopaminergic neuronal cell death, associated with intracellular α-synuclein (α-syn)–rich protein aggregates [termed “Lewy bodies” (LBs)], is a well-established characteristic of Parkinson’s disease (PD). Much evidence, accumulated from multiple experimental models, has suggested that α-syn plays a role in PD pathogenesis, not only as a trigger of pathology but also as a mediator of disease progression through pathological spreading. Here, we have used a machine learning–based approach to identify unique signatures of neurodegeneration in monkeys induced by distinct α-syn pathogenic structures derived from patients with PD. Unexpectedly, our results show that, in nonhuman primates, a small amount of singular α-syn aggregates is as toxic as larger amyloid fibrils present in the LBs, thus reinforcing the need for preclinical research in this species. Furthermore, our results provide evidence supporting the true multifactorial nature of PD, as multiple causes can induce a similar outcome regarding dopaminergic neurodegeneration.
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May 2020
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I05-ARPES
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Diamond Proposal Number(s):
[15822]
Open Access
Abstract: Van der Waals materials offer unprecedented control of electronic properties via stacking of different types of two-dimensional materials. A fascinating frontier, largely unexplored, is the stacking of strongly correlated phases of matter. We study 4Hb-TaS2, which naturally realizes an alternating stacking of 1T-TaS2 and 1H-TaS2 structures. The former is a well-known Mott insulator, which has recently been proposed to host a gapless spin-liquid ground state. The latter is a superconductor known to also host a competing charge density wave state. This raises the question of how these two components affect each other when stacked together. We find a superconductor with a Tc of 2.7 Kelvin and anomalous properties, of which the most notable one is a signature of time-reversal symmetry breaking, abruptly appearing at the superconducting transition. This observation is consistent with a chiral superconducting state.
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Mar 2020
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I05-ARPES
I09-Surface and Interface Structural Analysis
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Veronika
Sunko
,
F.
Mazzola
,
S.
Kitamura
,
S.
Khim
,
P.
Kushwaha
,
O. J.
Clark
,
M. D.
Watson
,
I.
Markovic
,
D.
Biswas
,
L.
Pourovskii
,
T. K.
Kim
,
T.-l.
Lee
,
P. K.
Thakur
,
H.
Rosner
,
A.
Georges
,
R.
Moessner
,
T.
Oka
,
A. P.
Mackenzie
,
P. D. C.
King
Diamond Proposal Number(s):
[19479, 17699]
Abstract: A nearly free electron metal and a Mott insulating state can be thought of as opposite ends of the spectrum of possibilities for the motion of electrons in a solid. Understanding their interaction lies at the heart of the correlated electron problem. In the magnetic oxide metal PdCrO2, nearly free and Mott-localized electrons exist in alternating layers, forming natural heterostructures. Using angle-resolved photoemission spectroscopy, quantitatively supported by a strong coupling analysis, we show that the coupling between these layers leads to an “intertwined” excitation that is a convolution of the charge spectrum of the metallic layer and the spin susceptibility of the Mott layer. Our findings establish PdCrO2 as a model system in which to probe Kondo lattice physics and also open new routes to use the a priori nonmagnetic probe of photoemission to gain insights into the spin susceptibility of correlated electron materials.
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Feb 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[15050, 14953]
Abstract: Precambrian fossils of fungi are sparse, and the knowledge of their early evolution and the role they played in the colonization of land surface are limited. Here, we report the discovery of fungi fossils in a 810 to 715 million year old dolomitic shale from the Mbuji-Mayi Supergroup, Democratic Republic of Congo. Syngenetically preserved in a transitional, subaerially exposed paleoenvironment, these carbonaceous filaments of ~5 μm in width exhibit low-frequency septation (pseudosepta) and high-angle branching that can form dense interconnected mycelium-like structures. Using an array of microscopic (SEM, TEM, and confocal laser scanning fluorescence microscopy) and spectroscopic techniques (Raman, FTIR, and XANES), we demonstrated the presence of vestigial chitin in these fossil filaments and document the eukaryotic nature of their precursor. Based on those combined evidences, these fossil filaments and mycelium-like structures are identified as remnants of fungal networks and represent the oldest, molecularly identified remains of Fungi.
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Jan 2020
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Tao
Ni
,
Fang
Jiao
,
Xiulian
Yu
,
Saša
Aden
,
Lucy
Ginger
,
Sophie I.
Williams
,
Fangfang
Bai
,
Vojtech
Prazak
,
Dimple
Karia
,
Phillip
Stansfeld
,
Peijun
Zhang
,
George
Munson
,
Gregor
Anderluh
,
Simon
Scheuring
,
Robert J. C.
Gilbert
Abstract: Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual phagocytes and whole organisms significantly more susceptible to bacterial pathogens. Here, we reveal the mechanism of perforin-2 activation and activity using atomic structures of pre-pore and pore assemblies, high-speed atomic force microscopy, and functional assays. Perforin-2 forms a pre-pore assembly in which its pore-forming domain points in the opposite direction to its membrane-targeting domain. Acidification then triggers pore formation, via a 180° conformational change. This novel and unexpected mechanism prevents premature bactericidal attack and may have played a key role in the evolution of all perforin family proteins.
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Jan 2020
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14843]
Open Access
Abstract: Adenoviruses are clinically important agents. They cause respiratory distress, gastroenteritis, and epidemic keratoconjunctivitis. As non-enveloped, double-stranded DNA viruses, they are easily manipulated, making them popular vectors for therapeutic applications, including vaccines. Species D adenovirus type 26 (HAdV-D26) is both a cause of EKC and other diseases and a promising vaccine vector. HAdV-D26–derived vaccines are under investigation as protective platforms against HIV, Zika, and respiratory syncytial virus infections and are in phase 3 clinical trials for Ebola. We recently demonstrated that HAdV-D26 does not use CD46 or Desmoglein-2 as entry receptors, while the putative interaction with coxsackie and adenovirus receptor is low affinity and unlikely to represent the primary cell receptor. Here, we establish sialic acid as a primary entry receptor used by HAdV-D26. We demonstrate that removal of cell surface sialic acid inhibits HAdV-D26 infection, and provide a high-resolution crystal structure of HAdV-D26 fiber-knob in complex with sialic acid.
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Sep 2019
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Krios II-Titan Krios II at Diamond
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Diamond Proposal Number(s):
[19832]
Open Access
Abstract: Quinol-dependent nitric oxide reductases (qNORs) are membrane-integrated, iron-containing enzymes of the denitrification pathway, which catalyze the reduction of nitric oxide (NO) to the major ozone destroying gas nitrous oxide (N2O). Cryo–electron microscopy structures of active qNOR from Alcaligenes xylosoxidans and an activity-enhancing mutant have been determined to be at local resolutions of 3.7 and 3.2 Å, respectively. They unexpectedly reveal a dimeric conformation (also confirmed for qNOR from Neisseria meningitidis) and define the active-site configuration, with a clear water channel from the cytoplasm. Structure-based mutagenesis has identified key residues involved in proton transport and substrate delivery to the active site of qNORs. The proton supply direction differs from cytochrome c–dependent NOR (cNOR), where water molecules from the cytoplasm serve as a proton source similar to those from cytochrome c oxidase.
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Aug 2019
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