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  • 1
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    Crystal structure of the 14-subunit RNA polymerase I (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-10-25
    Description: Protein biosynthesis depends on the availability of ribosomes, which in turn relies on ribosomal RNA production. In eukaryotes, this process is carried out by RNA polymerase I (Pol I), a 14-subunit enzyme, the activity of which is a major determinant of cell growth. Here we present the crystal structure of Pol I from Saccharomyces cerevisiae at 3.0 A resolution. The Pol I structure shows a compact core with a wide DNA-binding cleft and a tightly anchored stalk. An extended loop mimics the DNA backbone in the cleft and may be involved in regulating Pol I transcription. Subunit A12.2 extends from the A190 jaw to the active site and inserts a transcription elongation factor TFIIS-like zinc ribbon into the nucleotide triphosphate entry pore, providing insight into the role of A12.2 in RNA cleavage and Pol I insensitivity to alpha-amanitin. The A49-A34.5 heterodimer embraces subunit A135 through extended arms, thereby contacting and potentially regulating subunit A12.2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fernandez-Tornero, Carlos -- Moreno-Morcillo, Maria -- Rashid, Umar J -- Taylor, Nicholas M I -- Ruiz, Federico M -- Gruene, Tim -- Legrand, Pierre -- Steuerwald, Ulrich -- Muller, Christoph W -- England -- Nature. 2013 Oct 31;502(7473):644-9. doi: 10.1038/nature12636. Epub 2013 Oct 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, 28040 Madrid, Spain [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24153184" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Peptide Chain Elongation, Translational ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Subunits/*chemistry ; RNA Polymerase I/*chemistry ; RNA Polymerase II/chemistry ; RNA Polymerase III/chemistry ; Saccharomyces cerevisiae/*enzymology ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Structure of the T4 baseplate and its function in triggering sheath contraction (2016)
    Nature Publishing Group (NPG)
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    Publication Date: 2016-05-20
    Description: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taylor, Nicholas M I -- Prokhorov, Nikolai S -- Guerrero-Ferreira, Ricardo C -- Shneider, Mikhail M -- Browning, Christopher -- Goldie, Kenneth N -- Stahlberg, Henning -- Leiman, Petr G -- England -- Nature. 2016 May 18;533(7603):346-52. doi: 10.1038/nature17971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecole Polytechnique Federale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. ; Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, pr. 60-letiya Oktyabrya, 7 build. 2, 117312, Moscow, Russia. ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia. ; Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27193680" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Gravity waves simulated by high-resolution Whole Atmosphere Community Climate Model (2014)
    Wiley
    Details
    Publication Date: 2014-12-15
    Description: For the first time a mesoscale-resolving whole atmosphere general circulation model (GCM) has been developed, using the NCAR Whole Atmosphere Community Climate Model (WACCM) with ~0.25° horizontal resolution and 0.1 scale height vertical resolution above the middle stratosphere (higher resolution below). This is made possible by the high accuracy and high scalability of the spectral element dynamical core from the High-Order Method Modeling Environment (HOMME). For the simulated January-February period, the latitude-height structure and the magnitudes of the temperature variance compare well with those deduced from SABER observations. The simulation reveals the increasing dominance of gravity waves (GWs) at higher altitudes through both the height dependence of the kinetic energy spectra, which display a steeper slope (~-3) in the stratosphere and an increasingly shallower slope above, and the increasing spatial extent of GWs (including a planetary-scale extent of a concentric GW excited by a tropical cyclone) at higher altitudes. GW impacts on the large-scale flow is evaluated in terms of zonal mean zonal wind and tides: with no GW drag parameterized in the simulations, forcing by resolved GWs does reverse the summer mesospheric wind, albeit at an altitude higher than climatology, and only slows down the winter mesospheric wind without closing it. The hemispheric structures and magnitudes of diurnal and semidiurnal migrating tides compare favorably with observations.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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