New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.

/pdf/new-developments-in-the-atsas-program-package-for-small-4n7eqofqs5.pdf

New developments in the ATSAS program package for small-angle scattering data analysis

Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 A. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.

/pdf/structures-of-the-bacterial-ribosome-at-3-5-a-resolution-4pbqytwxq1.pdf

Structures of the bacterial ribosome at 3.5 Å resolution

The increased application of transcriptome-wide profiling approaches has led to an explosion in the number of documented long non-coding RNAs (lncRNAs). While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown. Early discoveries support a paradigm in which lncRNAs regulate transcription via chromatin modulation, but new functions are steadily emerging. Given the biochemical versatility of RNA, lncRNAs may be used for various tasks, including post-transcriptional regulation, organization of protein complexes, cell-cell signalling and allosteric regulation of proteins.

/pdf/rna-in-unexpected-places-long-non-coding-rna-functions-in-2cdl2nfa83.pdf

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

Summary: ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

Ribosomes translate genetic information encoded by messenger RNA into proteins. Many aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are much larger and intricate than their bacterial counterparts. We report the crystal structure of the 80S ribosome from the yeast Saccharomyces cerevisiae--including nearly all ribosomal RNA bases and protein side chains as well as an additional protein, Stm1--at a resolution of 3.0 angstroms. This atomic model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core, and describes all eukaryote-specific bridges between the two ribosomal subunits. It forms the structural framework for the design and analysis of experiments that explore the eukaryotic translation apparatus and the evolutionary forces that shaped it.

https://science.sciencemag.org/content/sci/early/2011/11/16/science.1212642.full.pdf

The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution

Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ribonucleoprotein particle. SRP recognizes signal sequences of nascent protein chains emerging from the ribosome. Subsequent binding of SRP leads to a pause in peptide elongation and to the ribosome docking to the membrane-bound SRP receptor. Here we present the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, solved to 12 A by cryo-electron microscopy, enables us to generate a molecular model of SRP in its functional conformation. The model shows how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation-factor-binding site of the ribosome, explaining its elongation arrest activity.

/pdf/structure-of-the-signal-recognition-particle-interacting-2njj1mwvag.pdf

Structure of the signal recognition particle interacting with the elongation-arrested ribosome

Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA–eEF1A–GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release.

/pdf/structure-of-eef3-and-the-mechanism-of-transfer-rna-release-46oemp2n5d.pdf

Structure of eEF3 and the Mechanism of Transfer RNA Release From the E-Site

Niklas Luhmann hat in seinem Buch Liebe als Passion mit der Herausbildung der passionierten Liebe ein Beispiel fur die Beschreibung eines Mediums der Kommunikation vorgestellt, das stratifikatorische Differenzen umgehen kann. Pierre Bourdieu dagegen hat in seinen Auβerungen zum Thema Liebe zu erkennen gegeben, dass sich deren Integrationskraft nicht ohne die unterschiedlichen Kosten der Inklusion je nach Klassenlage und Struktur des symbolischen Kapitals beschreiben lasst. Fur den im 17. Jahrhundert entstandenen Liebescode lasst sich mit der feldsoziologischen Methode zeigen, dass eine neue soziale Reproduktion im Feld der Macht entstand, die erst die passionierte Liebe zum Effekt hatte. Die Vererbung okonomischen Kapitals bedurfte der zunehmenden Legitimation durch kulturelles Kapital. Die im 17. Jahrhundert entstandene Liebesliteratur in den Literatursalons stellte einerseits diese Kultur zur Verfugung, stutzte aber auch andererseits die Emanzipation von Frauen und die Integration burgerlicher Autoren im Feld der Macht. Fur die Feldsoziologie wird damit gezeigt, dass ihre Theorie der Differenzierung spezifischer sozialer Felder der Kulturproduktion auch auf das Verstandnis vormoderner Gesellschaften anwendbar ist.

Liebe: Medium der Kommunikation oder Symbolisches Kapital der Sozialen Reproduktion?

Ästhetische Erfahrung der Intermedialität: Zum Transfer künstlerischer Avantgarden und 'illegitimer' Kunst im Zeitalter von Massenkommunikation und Internet

Thomas Becker

Papers

Structure of the signal recognition particle interacting with the elongation-arrested ribosome

Structure of eEF3 and the Mechanism of Transfer RNA Release From the E-Site

Liebe: Medium der Kommunikation oder Symbolisches Kapital der Sozialen Reproduktion?

Ästhetische Erfahrung der Intermedialität: Zum Transfer künstlerischer Avantgarden und 'illegitimer' Kunst im Zeitalter von Massenkommunikation und Internet