Biology subjects

Raunser, S.

Publications and source records attributed to Raunser, S..

3 recordsLinked to original sources

bioRxiv2018

SPHIRE-crYOLO: A fast and well-centering automated particle picker for cryo-EM

Selecting particles from digital micrographs is an essential step in single particle electron cryomicroscopy (cryo-EM). Since manual selection is a tedious and time-consuming process, many automatic particle pickers have been developed. However, they have problems especially with non-ideal datasets. Here, we present a novel automated particle picking software called crYOLO, which is based on the deep learning object detection system \"You Only Look Once\" (YOLO). After training the network with 500 - 2,500 particles per dataset, it automatically selects the particles with high accuracy and precision reaching a speed of up to six micrographs per second. Importantly, we show that crYOLO can be trained to select previously unseen datasets paving the way for completely automated \"on-the-fly\" cryo-EM data pre-processing during data acquisition. CrYOLO is available as standalone program under http://sphire.mpg.de/ and will be part of the image processing workflow in SPHIRE.

biophysics↗

bioRxiv2018

Membrane insertion of α-xenorhabdolysin in near-atomic detail

-Xenorhabdolysins (Xax) are -pore-forming toxins (-PFT) from pathogenic bacteria that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens as an offensive or defensive mechanism to attack host cells. Due to the lack of structural information, the molecular mechanism of action of Xax toxins is poorly understood. Here, we report the cryo-EM structure of the XaxAB pore complex from Xenorhabdus nematophila at an average resolution of 4.0 [A] and the crystal structures of the soluble monomers of XaxA and XaxB at 2.5 [A] and 3.4 [A], respectively. The structures reveal that XaxA and XaxB are built similarly and appear as heterodimers in the 12-15 subunits containing pore. The structure of the XaxAB pore represents therefore the first structure of a bi-component -PFT. Major conformational changes in XaxB, including the swinging out of an amphipathic helix are responsible for membrane insertion. XaxA acts as an activator and stabilizer for XaxB that forms the actual transmembrane pore. Based on our results, we propose a novel structural model for the mechanism of action of Xax toxins.

molecular biology↗

bioRxiv2018

Electron cryo-microscopy structure of the canonical TRPC4 ion channel

Canonical transient receptor channels (TRPC) are non-selective cation channels. They are involved in receptor-operated Ca2+ signaling and have been proposed to act as store-operated channels (SOC). Their malfunction is related to cardiomyopathies and their modulation by small molecules has been shown to be effective against renal cancer cells. The molecular mechanism underlying the complex activation and regulation is poorly understood. Here, we report the electron cryo-microscopy structure of zebrafish TRPC4 in its unliganded (apo), closed state at an overall resolution of 3.6 [A]. The structure reveals the molecular architecture of the cation conducting pore, including the selectivity filter and lower gate. The cytoplasmic domain contains two key hubs that have been shown to interact with modulating proteins. Structural comparisons with other TRP channels give novel insights into the general architecture and domain organization of this superfamily of channels and help to understand their function and pharmacology.

biochemistry↗