Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8

The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain. However, the molecular basis for this complex regulatory network has remained elusive. Here, we present cryo-electron microscopy reconstructions of human SMG1-9 and SMG1-8-9 complexes bound to either a SMG1 inhibitor or a non-hydrolyzable ATP analog at overall resolutions ranging from 2.8 to 3.6 angstrom. These structures reveal the basis with which a small molecule inhibitor preferentially targets SMG1 over other PIKKs. By comparison with our previously reported substrate-bound structure (Langer et al.,2020), we show that the SMG1 insertion domain can exert an autoinhibitory function by directly blocking the substrate-binding path as well as overall access to the SMG1 kinase active site. Together with biochemical analysis, our data indicate that SMG1 autoinhibition is stabilized by the presence of SMG8. Our results explain the specific inhibition of SMG1 by an ATP-competitive small molecule, provide insights into regulation of its kinase activity within the NMD pathway, and expand the understanding of PIKK regulatory mechanisms in general.Acknowledgements: Daniel Bollschweiler and Tillman Schäfer at the MPIB cryo-EM facility for help with EM data collection and Barbara Steigenberger and Elisabeth Weyher at MPIB biochemistry core facility for carrying out mass spectrometry

Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity

PI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of an RNA quality control pathway, termed nonsense-mediated mRNA decay (NMD), by phosphorylating the NMD factor UPF1. Phosphorylation of UPF1 occurs in its unstructured N- and C-terminal regions at Serine/Threonine-Glutamine (SQ) motifs. How SMG1 and other PIKKs specifically recognize SQ motifs has remained unclear. Here, we present a cryo-electron microscopy (cryo-EM) reconstruction of a human SMG1-8-9 kinase complex bound to a UPF1 phosphorylation site at an overall resolution of 2.9 angstrom. This structure provides the first snapshot of a human PIKK with a substrate-bound active site. Together with biochemical assays, it rationalizes how SMG1 and perhaps other PIKKs specifically phosphorylate Ser/Thr-containing motifs with a glutamine residue at position +1 and a hydrophobic residue at position -1, thus elucidating the molecular basis for phosphorylation site recognition

Scotland, Catalonia and the “right” to self-determination: a comment suggested by Kathryn Crameri’s “Do Catalans Have the Right to Decide?

No abstract available

Muon Spin Relaxation and Susceptibility Studies of Pure and Doped Spin 1/2 Kagom\'{e}-like system (Cux_xZn1−x_{1-x})3_{3}V2_{2}O7_7(OH)2_{2} 2H2_2O

Muon spin relaxation ($\mu$SR) and magnetic susceptibility measurements have been performed on the pure and diluted spin 1/2 kagom\'{e} system (Cu$_x$Zn$_{1-x}$)$_{3}$V$_{2}$O$_7$(OH)$_{2}$ 2H$_2$O. In the pure $x=1$ system we found a slowing down of Cu spin fluctuations with decreasing temperature towards $T \sim 1$ K, followed by slow and nearly temperature-independent spin fluctuations persisting down to $T$ = 50 mK, indicative of quantum fluctuations. No indication of static spin freezing was detected in either of the pure ($x$=1.0) or diluted samples. The observed magnitude of fluctuating fields indicates that the slow spin fluctuations represent an intrinsic property of kagom\'e network rather than impurity spins.Comment: 4 pges, 4 color figures, Phys. Rev. Lett. in pres

Doping and temperature dependence of electron spectrum and quasiparticle dispersion in doped bilayer cuprates

Within the t-t'-J model, the electron spectrum and quasiparticle dispersion in doped bilayer cuprates in the normal state are discussed by considering the bilayer interaction. It is shown that the bilayer interaction splits the electron spectrum of doped bilayer cuprates into the bonding and antibonding components around the $(\pi,0)$ point. The differentiation between the bonding and antibonding components is essential, which leads to two main flat bands around the $(\pi,0)$ point below the Fermi energy. In analogy to the doped single layer cuprates, the lowest energy states in doped bilayer cuprates are located at the $(\pi/2,\pi/2)$ point. Our results also show that the striking behavior of the electronic structure in doped bilayer cuprates is intriguingly related to the bilayer interaction together with strong coupling between the electron quasiparticles and collective magnetic excitations.Comment: 9 pages, 4 figures, updated references, added figures and discussions, accepted for publication in Phys. Rev.

Site-Dilution in quasi one-dimensional antiferromagnet Sr2(Cu1-xPdx)O3: reduction of Neel Temperature and spatial distribution of ordered moment sizes

We investigate the Neel temperature of Sr2CuO3 as a function of the site dilution at the Cu (S=1/2) sites with Pd (S=0), utilizing the muon spin relaxation (muSR) technique. The Neel temperature, which is Tn=5.4K for the undoped system, becomes significantly reduced for less than one percent of doping Pd, giving a support for the previous proposal for the good one-dimensionality. The Pd concentration dependence of the Neel temperature is compared with a recent theoretical study (S. Eggert, I. Affleck and M.D.P. Horton, Phys. Rev. Lett. 89, 47202 (2002)) of weakly coupled one-dimensional antiferromagnetic chains of S=1/2 spins, and a quantitative agreement is found. The inhomogeneity of the ordered moment sizes is characterized by the muSR time spectra. We propose a model that the ordered moment size recovers away from the dopant S=0 sites with a recovery length of \xi = 150-200 sites. The origin of the finite recovery length \xi for the gapless S=1/2 antiferromagnetic chain is compared to the estimate based on the effective staggered magnetic field from the neighboring chains.Comment: 10 pages, 9 figures, submitted to PR

The Dynamical Behaviors in (2+1)-Dimensional Gross-Neveu Model with a Thirring Interaction

We analyze (2+1)-dimensional Gross-Neveu model with a Thirring interaction, where a vector-vector type four-fermi interaction is on equal terms with a scalar-scalar type one. The Dyson-Schwinger equation for fermion self-energy function is constructed up to next-to-leading order in 1/N expansion. We determine the critical surface which is the boundary between a broken phase and an unbroken one in ($\alpha_c,~ \beta_c,~ N_c$) space. It is observed that the critical behavior is mainly controlled by Gross-Neveu coupling $\alpha_c$ and the region of the broken phase is separated into two parts by the line $\alpha_c=\alpha_c^*(=\frac{8}{\pi^2})$. The mass function is strongly dependent upon the flavor number N for $\alpha > \alpha_c^*$, while weakly for $\alpha \alpha_c^*$, the critical flavor number $N_c$ increases as Thirring coupling $\beta$ decreases. By driving the CJT effective potential, we show that the broken phase is energetically preferred to the symmetric one. We discuss the gauge dependence of the mass function and the ultra-violet property of the composite operators.Comment: 19 pages, LaTex, 6 ps figure files(uuencoded in seperate file

Phase separation and suppression of critical dynamics at quantum transitions of itinerant magnets: MnSi and (Sr1−x_{1-x}Cax_{x})RuO3_{3}

Quantum phase transitions (QPTs) have been studied extensively in correlated electron systems. Characterization of magnetism at QPTs has, however, been limited by the volume-integrated feature of neutron and magnetization measurements and by pressure uncertainties in NMR studies using powderized specimens. Overcoming these limitations, we performed muon spin relaxation ($\mu$SR) measurements which have a unique sensitivity to volume fractions of magnetically ordered and paramagnetic regions, and studied QPTs from itinerant heli/ferro magnet to paramagnet in MnSi (single-crystal; varying pressure) and (Sr$_{1-x}$Ca$_{x}$)RuO$_{3}$ (ceramic specimens; varying $x$). Our results provide the first clear evidence that both cases are associated with spontaneous phase separation and suppression of dynamic critical behavior, revealed a slow but dynamic character of the ``partial order'' diffuse spin correlations in MnSi above the critical pressure, and, combined with other known results in heavy-fermion and cuprate systems, suggest a possibility that a majority of QPTs involve first-order transitions and/or phase separation.Comment: 11 pages, 4 figures, 21 authors, to appear in Nature Physic

Muon Spin Relaxation Studies of Magnetic-Field-Induced Effects in High-TcT_{c} Superconductors

Muon spin relaxation ($\mu$SR) measurements in high transverse magnetic fields ($\parallel \hat c$) revealed strong field-induced quasi-static magnetism in the underdoped and Eu doped (La,Sr)$_{2}$CuO$_{4}$ and La$_{1.875}$Ba$_{0.125}$CuO$_{4}$, existing well above $T_{c}$ and $T_{N}$. The susceptibility-counterpart of Cu spin polarization, derived from the muon spin relaxation rate, exhibits a divergent behavior towards $T \sim 25$ K. No field-induced magnetism was detected in overdoped La$_{1.81}$Sr$_{0.19}$CuO$_{4}$, optimally doped Bi2212, and Zn-doped YBa$_{2}$Cu$_{3}$O$_{7}$.Comment: 4 pages, 4 color figure