Abstract:Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detail… Show more
“…Therefore, this abstraction was created to improve the communication between developers through establishing a common language when talking about specific SIMPLE functionalities. This kind of abstraction ought to be helpful also for those developing packages of packages, such as Scipion ( de la Rosa-Trevín et al, 2016 , Gomez-Blanco et al, 2018 ) or Appion ( Lander et al, 2009 ), allowing more rapid integration when new versions of SIMPLE are released. Furthermore, it could provide a framework for integrating other functionalities than SIMPLE within the GUI in the future.…”
Section: Resultsmentioning
confidence: 99%
“…This is escalating the computational demands but opens the possibility of rapid, definitive assessment of samples at the 2D level within the first hour of data collection. Several developers are working to provide solutions for this real-time problem ( Gomez-Blanco et al, 2018 , Maluenda et al, 2019 , Tegunov and Cramer, 2019 , Wagner and Raunser, 2020 ). We here describe SIMPLE 3.0, which we have developed to managed data flow in the Central Oxford Structural Molecular Imaging Centre over the last two years.…”
Section: Introductionmentioning
confidence: 99%
“…SIMPLE 3.0 runs on relatively cheap and scalable CPU resources thus allowing use of existing computer resources to support real-time processing of SP data ( Table 1 , Results below). In contrast to developments that provide data organization tools and interfaces to other software, such as Scipion ( Gomez-Blanco et al, 2018 , Maluenda et al, 2019 ) and Focus ( Biyani et al, 2017 ), our SIMPLE 3.0 suite consists of a collection of novel image processing algorithms that have been tailored and optimized for use in a stream scenario.…”
“…Therefore, this abstraction was created to improve the communication between developers through establishing a common language when talking about specific SIMPLE functionalities. This kind of abstraction ought to be helpful also for those developing packages of packages, such as Scipion ( de la Rosa-Trevín et al, 2016 , Gomez-Blanco et al, 2018 ) or Appion ( Lander et al, 2009 ), allowing more rapid integration when new versions of SIMPLE are released. Furthermore, it could provide a framework for integrating other functionalities than SIMPLE within the GUI in the future.…”
Section: Resultsmentioning
confidence: 99%
“…This is escalating the computational demands but opens the possibility of rapid, definitive assessment of samples at the 2D level within the first hour of data collection. Several developers are working to provide solutions for this real-time problem ( Gomez-Blanco et al, 2018 , Maluenda et al, 2019 , Tegunov and Cramer, 2019 , Wagner and Raunser, 2020 ). We here describe SIMPLE 3.0, which we have developed to managed data flow in the Central Oxford Structural Molecular Imaging Centre over the last two years.…”
Section: Introductionmentioning
confidence: 99%
“…SIMPLE 3.0 runs on relatively cheap and scalable CPU resources thus allowing use of existing computer resources to support real-time processing of SP data ( Table 1 , Results below). In contrast to developments that provide data organization tools and interfaces to other software, such as Scipion ( Gomez-Blanco et al, 2018 , Maluenda et al, 2019 ) and Focus ( Biyani et al, 2017 ), our SIMPLE 3.0 suite consists of a collection of novel image processing algorithms that have been tailored and optimized for use in a stream scenario.…”
“… Resolution was computed using the version of Mono Res embedded within Scipion ( Gomez-Blanco et al, 2018 ). The color bars show the local resolution on each surface in Ångstroms.…”
Striated muscle thick filaments are composed of myosin II and several non-myosin proteins. Myosin II’s long α-helical coiled-coil tail forms the dense protein backbone of filaments, whereas its N-terminal globular head containing the catalytic and actin-binding activities extends outward from the backbone. Here, we report the structure of thick filaments of the flight muscle of the fruit fly Drosophila melanogaster at 7 Å resolution. Its myosin tails are arranged in curved molecular crystalline layers identical to flight muscles of the giant water bug Lethocerus indicus. Four non-myosin densities are observed, three of which correspond to ones found in Lethocerus; one new density, possibly stretchin-mlck, is found on the backbone outer surface. Surprisingly, the myosin heads are disordered rather than ordered along the filament backbone. Our results show striking myosin tail similarity within flight muscle filaments of two insect orders separated by several hundred million years of evolution.
“…The dose per frame was 1.07 e/Å 2 , and we used defoci from 0.8 to 2.6 µm. The movies were aligned with MotionCor2 (42) within the Scipion framework(43). Contrast transfer function was estimated by CTFFind 4.1.5(44), and the resulting 2786 good images were used for further data processing.…”
AbstractMalaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodium spp.) that cause the disease depend upon an unconventional actomyosin motor for both gliding motility and host cell invasion. The motor system, often referred to as the glideosome complex, remains to be understood in molecular terms and is an attractive target for new drugs that might block the infection pathway. Here, we present the first high-resolution structure of the actomyosin motor complex from Plasmodium falciparum. Our structure includes the malaria parasite actin filament (PfAct1) complexed with the myosin motor (PfMyoA) and its two associated light-chains. The high-resolution core structure reveals the PfAct1:PfMyoA interface in atomic detail, while at lower-resolution, we visualize the PfMyoA light-chain binding region, including the essential light chain (PfELC) and the myosin tail interacting protein (PfMTIP). Finally, we report a bare PfAct1 filament structure at an improved resolution, which gives new information about the nucleotide-binding site, including the orientation of the ATP/ADP sensor, Ser15, and the presence of a channel, which we propose as a possible phosphate exit path after ATP hydrolysis.Significance statementWe present the first structure of the malaria parasite motor complex; actin 1 (PfAct1) and myosin A (PfMyoA) with its two light chains. We also report a high-resolution structure of filamentous PfAct1 that reveals new atomic details of the ATPase site, including a channel, which may provide an exit route for phosphate and explain why phosphate release is faster in PfAct1 compared to canonical actins. PfAct1 goes through no conformational changes upon PfMyoA binding. Our PfMyoA structure also superimposes with a recent crystal structure of PfMyoA alone, though there are small but important conformational changes at the interface. Our structures serve as an excellent starting point for drug design against malaria, which is one of the most devastating infectious diseases.
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