Project description:RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. However, it is unclear how most RNA helicases interact with ribosome assembly intermediates or participate in other cell processes to regulate ribosome assembly. SrmB is a DEAD-box helicase that acts early in the ribosome assembly process, although very little is known about its mechanism of action. Here, we use a combined quantitative mass spectrometry/cryo-electron microscopy approach to detail the protein inventory, rRNA modification state, and structures of 40S ribosomal intermediates that form upon SrmB deletion. We show that the binding site of SrmB is unperturbed by SrmB deletion, but the peptidyl transferase center, the uL7/12 stalk, and 30S contact sites all show severe assembly defects. Taking into account existing data on SrmB function and the experiments presented here, we propose several mechanisms by which SrmB could guide assembling particles from kinetic traps to competent subunits during the 50S ribosome assembly process.
Project description:Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we present the electron cryo-microscopy (cryo-EM) structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces cerevisiae at 18 angstrom resolution. We obtained cryo-EM reconstructions of preribosomal complexes lacking individual components to define the positions of all seven AFs bound to this intermediate. These late-binding AFs are positioned to prevent each step in the translation initiation pathway. Together, they obstruct the binding sites for initiation factors, prevent the opening of the messenger RNA channel, block 60S subunit joining, and disrupt the decoding site. These redundant mechanisms probably ensure that pre-40S particles do not enter the translation pathway, which would result in their rapid degradation.
Project description:This paper contains a vanadium redox flow battery stack with an electrode surface area 40 cm2 test data. The aim of the study was to characterize the performance of the stack of the original design. The dataset include three series of galvanostatic charge-discharge cycling in the potential region 8-16 V with current densities 75, 150 and 200 mA/cm2 for 100 cycles. Coulomb, voltaic, energy efficiencies and capacity utilization coefficient are also provided for all three series.
Project description:The three conserved core subunits of the cytochrome c oxidase are encoded by mitochondria in close to all eukaryotes. The Cox2 subunit spans the inner membrane twice, exposing the N and C termini to the intermembrane space. For this, the N terminus is exported cotranslationally by Oxa1 and subsequently undergoes proteolytic maturation in Saccharomyces cerevisiae Little is known about the translocation of the C terminus, but Cox18 has been identified to be a critical protein in this process. Here we find that the scaffold protein Cox20, which promotes processing of Cox2, is in complex with the ribosome receptor Mba1 and translating mitochondrial ribosomes in a Cox2-dependent manner. The Mba1-Cox20 complex accumulates when export of the C terminus of Cox2 is blocked by the loss of the Cox18 protein. While Cox20 engages with Cox18, Mba1 is no longer present at this stage. Our analyses indicate that Cox20 associates with nascent Cox2 and Mba1 to promote Cox2 maturation cotranslationally. We suggest that Mba1 stabilizes the Cox20-ribosome complex and supports the handover of Cox2 to the Cox18 tail export machinery.
Project description:Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations into different groups through computational classification. However, there is a dearth of tools for surveying the heterogeneity landscape, quantitatively analyzing heterogeneous particle populations after classification, deciding how many unique classes are represented by the data, and accurately cross-comparing reconstructions. Here, we develop a workflow that contains discovery and analysis modules to quantitatively mine cryo-EM data for sets of structures with maximal diversity. This workflow was applied to a dataset of E. coli 50S ribosome assembly intermediates, which are characterized by significant structural heterogeneity. We identified more detailed branchpoints in the assembly process and characterized the interactions of an assembly factor with immature intermediates. While the tools described here were developed for ribosome assembly, they should be broadly applicable to the analysis of other heterogeneous cryo-EM datasets.
Project description:We provide a database containing shot scale annotations (i.e., the apparent distance of the camera from the subject of a filmed scene) for more than 792,000 image frames. Frames belong to 124 full movies from the entire filmographies by 6 important directors: Martin Scorsese, Jean-Luc Godard, Béla Tarr, Federico Fellini, Michelangelo Antonioni, and Ingmar Bergman. Each frame, extracted from videos at 1 frame per second, is annotated on the following scale categories: Extreme Close Up (ECU), Close Up (CU), Medium Close Up (MCU), Medium Shot (MS), Medium Long Shot (MLS), Long Shot (LS), Extreme Long Shot (ELS), Foreground Shot (FS), and Insert Shots (IS). Two independent coders annotated all frames from the 124 movies, whilst a third one checked their coding and made decisions in cases of disagreement. The CineScale database enables AI-driven interpretation of shot scale data and opens to a large set of research activities related to the automatic visual analysis of cinematic material, such as the automatic recognition of the director's style, or the unfolding of the relationship between shot scale and the viewers' emotional experience. To these purposes, we also provide the model and the code for building a Convolutional Neural Network (CNN) architecture for automated shot scale recognition. All this material is provided through the project website, where video frames can also be requested to authors, for research purposes under fair use.