I24-Microfocus Macromolecular Crystallography
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Angeliki
Ditsiou
,
Chiara
Cilibrasi
,
Nikiana
Simigdala
,
Athanasios
Papakyriakou
,
Leanne
Milton-harris
,
Viviana
Vella
,
Joanne E.
Nettleship
,
Jae Ho
Lo
,
Shivani
Soni
,
Goar
Smbatyan
,
Panagiota
Ntavelou
,
Teresa
Gagliano
,
Maria Chiara
Iachini
,
Sahir
Khurshid
,
Thomas
Simon
,
Lihong
Zhou
,
Storm
Hassell-hart
,
Philip
Carter
,
Laurence H.
Pearl
,
Robin L.
Owen
,
Raymond J.
Owens
,
S. Mark
Roe
,
Naomi E.
Chayen
,
Heinz-josef
Lenz
,
John
Spencer
,
Chrisostomos
Prodromou
,
Apostolos
Klinakis
,
Justin
Stebbing
,
Georgios
Giamas
Diamond Proposal Number(s):
[14493]
Open Access
Abstract: Elucidating signaling driven by lemur tyrosine kinase 3 (LMTK3) could help drug development. Here, we solve the crystal structure of LMTK3 kinase domain to 2.1Å resolution, determine its consensus motif and phosphoproteome, unveiling in vitro and in vivo LMTK3 substrates. Via high-throughput homogeneous time-resolved fluorescence screen coupled with biochemical, cellular, and biophysical assays, we identify a potent LMTK3 small-molecule inhibitor (C28). Functional and mechanistic studies reveal LMTK3 is a heat shock protein 90 (HSP90) client protein, requiring HSP90 for folding and stability, while C28 promotes proteasome-mediated degradation of LMTK3. Pharmacologic inhibition of LMTK3 decreases proliferation of cancer cell lines in the NCI-60 panel, with a concomitant increase in apoptosis in breast cancer cells, recapitulating effects of LMTK3 gene silencing. Furthermore, LMTK3 inhibition reduces growth of xenograft and transgenic breast cancer mouse models without displaying systemic toxicity at effective doses. Our data reinforce LMTK3 as a druggable target for cancer therapy.
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Nov 2020
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I19-Small Molecule Single Crystal Diffraction
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Weihua
Ning
,
Jinke
Bao
,
Yuttapoom
Puttisong
,
Fabrizo
Moro
,
Libor
Kobera
,
Seiya
Shimono
,
Linqin
Wang
,
Fuxiang
Ji
,
Maria
Cuartero
,
Shogo
Kawaguchi
,
Sabina
Abbrent
,
Hiroki
Ishibashi
,
Roland
De Marco
,
Irina A.
Bouianova
,
Gaston A.
Crespo
,
Yoshiki
Kubota
,
Jiri
Brus
,
Duck Young
Chung
,
Licheng
Sun
,
Weimin M.
Chen
,
Mercouri G.
Kanatzidis
,
Feng
Gao
Diamond Proposal Number(s):
[20805]
Open Access
Abstract: Spintronics holds great potential for next-generation high-speed and low–power consumption information technology. Recently, lead halide perovskites (LHPs), which have gained great success in optoelectronics, also show interesting magnetic properties. However, the spin-related properties in LHPs originate from the spin-orbit coupling of Pb, limiting further development of these materials in spintronics. Here, we demonstrate a new generation of halide perovskites, by alloying magnetic elements into optoelectronic double perovskites, which provide rich chemical and structural diversities to host different magnetic elements. In our iron-alloyed double perovskite, Cs2Ag(Bi:Fe)Br6, Fe3+ replaces Bi3+ and forms FeBr6 clusters that homogenously distribute throughout the double perovskite crystals. We observe a strong temperature-dependent magnetic response at temperatures below 30 K, which is tentatively attributed to a weak ferromagnetic or antiferromagnetic response from localized regions. We anticipate that this work will stimulate future efforts in exploring this simple yet efficient approach to develop new spintronic materials based on lead-free double perovskites.
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Nov 2020
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I23-Long wavelength MX
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Open Access
Abstract: K2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K2Ps is unknown. Here, combining K2P2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K2P C-type gating. These asymmetric order-disorder transitions, enabled by the K2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K2P SF2-M4 loop and conserved “M3 glutamate network,” and are suppressed by the K2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K2P channel modulator development.
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Oct 2020
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I03-Macromolecular Crystallography
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Sarah V.
Faull
,
Emma L. K.
Elliston
,
Bibek
Gooptu
,
Alistair M.
Jagger
,
Ibrahim
Aldobiyan
,
Adam
Redzej
,
Magd
Badaoui
,
Nina
Heyer-chauhan
,
S. Tamir
Rashid
,
Gary M.
Reynolds
,
David H.
Adams
,
Elena
Miranda
,
Elena V.
Orlova
,
James A.
Irving
,
David A.
Lomas
Diamond Proposal Number(s):
[17201]
Open Access
Abstract: The serpinopathies are among a diverse set of conformational diseases that involve the aberrant self-association of proteins into ordered aggregates. α1-Antitrypsin deficiency is the archetypal serpinopathy and results from the formation and deposition of mutant forms of α1-antitrypsin as “polymer” chains in liver tissue. No detailed structural analysis has been performed of this material. Moreover, there is little information on the relevance of well-studied artificially induced polymers to these disease-associated molecules. We have isolated polymers from the liver tissue of Z α1-antitrypsin homozygotes (E342K) who have undergone transplantation, labeled them using a Fab fragment, and performed single-particle analysis of negative-stain electron micrographs. The data show structural equivalence between heat-induced and ex vivo polymers and that the intersubunit linkage is best explained by a carboxyl-terminal domain swap between molecules of α1-antitrypsin.
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Oct 2020
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B21-High Throughput SAXS
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[16258]
Open Access
Abstract: Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin’s Gly76. Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD+. Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD+ bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.
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Sep 2020
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I15-Extreme Conditions
I22-Small angle scattering & Diffraction
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Danilo
Di Genova
,
Richard A.
Brooker
,
Heidy M.
Mader
,
James W. E.
Drewitt
,
Alessandro
Longo
,
Joachim
Deubener
,
Daniel R.
Neuville
,
Sara
Fanara
,
Olga
Shebanova
,
Simon
Anzellini
,
Fabio
Arzilli
,
Emily C.
Bamber
,
Louis
Hennet
,
Giuseppe
La Spina
,
Nobuyoshi
Miyajima
Diamond Proposal Number(s):
[17615, 20447]
Open Access
Abstract: Although gas exsolution is a major driving force behind explosive volcanic eruptions, viscosity is critical in controlling the escape of bubbles and switching between explosive and effusive behavior. Temperature and composition control melt viscosity, but crystallization above a critical volume (>30 volume %) can lock up the magma, triggering an explosion. Here, we present an alternative to this well-established paradigm by showing how an unexpectedly small volume of nano-sized crystals can cause a disproportionate increase in magma viscosity. Our in situ observations on a basaltic melt, rheological measurements in an analog system, and modeling demonstrate how just a few volume % of nanolites results in a marked increase in viscosity above the critical value needed for explosive fragmentation, even for a low-viscosity melt. Images of nanolites from low-viscosity explosive eruptions and an experimentally produced basaltic pumice show syn-eruptive growth, possibly nucleating a high bubble number density.
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Sep 2020
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Krios I-Titan Krios I at Diamond
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B.
Vollmer
,
V.
Prazak
,
D.
Vasishtan
,
E. E.
Jefferys
,
A.
Hernandez-duran
,
M.
Vallbracht
,
B. G.
Klupp
,
T. C.
Mettenleiter
,
M.
Backovic
,
F. A.
Rey
,
M.
Topf
,
K.
Grunewald
Open Access
Abstract: Cell entry of enveloped viruses requires specialized viral proteins that mediate fusion with the host membrane by substantial structural rearrangements from a metastable pre- to a stable postfusion conformation. This metastability renders the herpes simplex virus 1 (HSV-1) fusion glycoprotein B (gB) highly unstable such that it readily converts into the postfusion form, thereby precluding structural elucidation of the pharmacologically relevant prefusion conformation. By identification of conserved sequence signatures and molecular dynamics simulations, we devised a mutation that stabilized this form. Functionally locking gB allowed the structural determination of its membrane-embedded prefusion conformation at sub-nanometer resolution and enabled the unambiguous fit of all ectodomains. The resulting pseudo-atomic model reveals a notable conservation of conformational domain rearrangements during fusion between HSV-1 gB and the vesicular stomatitis virus glycoprotein G, despite their very distant phylogeny. In combination with our comparative sequence-structure analysis, these findings suggest common fusogenic domain rearrangements in all class III viral fusion proteins.
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Sep 2020
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[15836, 21777, 23510]
Open Access
Abstract: Meiotic reductional division depends on the synaptonemal complex (SC), a supramolecular protein assembly that mediates homologous chromosomes synapsis and promotes crossover formation. The mammalian SC has eight structural components, including SYCE1, the only central element protein with known causative mutations in human infertility. We combine mouse genetics, cellular, and biochemical studies to reveal that SYCE1 undergoes multivalent interactions with SC component SIX6OS1. The N terminus of SIX6OS1 binds and disrupts SYCE1’s core dimeric structure to form a 1:1 complex, while their downstream sequences provide a distinct second interface. These interfaces are separately disrupted by SYCE1 mutations associated with nonobstructive azoospermia and premature ovarian failure (POF), respectively. Mice harboring SYCE1’s POF mutation and a targeted deletion within SIX6OS1’s N terminus are infertile with failure of chromosome synapsis. We conclude that both SYCE1-SIX6OS1 binding interfaces are essential for SC assembly, thus explaining how SYCE1’s reported clinical mutations give rise to human infertility.
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Sep 2020
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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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