Showing papers in "Journal of Structural Biology in 2017"

TL;DR: A “dose-symmetric tilt-scheme” that begins at low tilt and then alternates between increasingly positive and negative tilts maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications.

TL;DR: Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes, and a user interface for batch processing of tilt series is added to the Etomo program in IMOD.

TL;DR: This work describes a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION that is capable of reconstructing structures to near-atomic resolution and calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space.

TL;DR: This work presents a comprehensive description of a cryo-sample preparation workflow incorporating additional conductive-coating procedures, and discusses optimized FIB milling strategies adapted from material science and each critical step required to produce homogeneously thin, non-charging FIB lamellas.

TL;DR: A user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD is presented and it is found that high-resolution structures can be obtained with much smaller subtomogram averaging datasets than are required using 2D- CTF.

TL;DR: Focus provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions.

TL;DR: High-resolution structures are used to illustrate the overall architecture of AIM2 inflammasome and its assembly and regulatory mechanisms, including helical filaments nucleated by upstream molecules, rather than stoichiometric complexes.

TL;DR: Time-resolvedcryo-electron microscopy combines the known advantages of single-particle cryo-EM in visualizing molecular structure with the ability to dissect the time progress of a reaction between molecules in vitro.

TL;DR: This work streamline data processing for subtomogram averaging by introducing an archiving system, Dynamo Catalogue, which manages tomographic data from multiple tomograms and allows visual feedback during all processing steps, including particle picking, extraction, alignment and classification.

TL;DR: Current trends in single-molecule force spectroscopy include customized fingerprint domains, peptide tags for site-specific covalent surface attachment, and polyproteins that are formed through mechanostable receptor-ligand interactions.

TL;DR: The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment and is combined with a transfer shuttle for contamination-free loading of the specimen.

TL;DR: A sample preparation method that requires only 3-20nL of sample to prepare a cryo-EM grid and will enable alternative electron microscopy approaches, such as single-cell visual proteomics, is presented.

TL;DR: This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level.

TL;DR: A new workbench named SuRVoS (Super-Region Volume Segmentation), within this software, a volume to be segmented is first partitioned into hierarchical segmentation layers and is then interactively segmented with the user's knowledge input in the form of training annotations.

TL;DR: This study demonstrates that the VPP is a valuable tool for subtomogram analysis, because it enables improved performance and efficiency in terms of structure localization and number of subtomograms required for a given resolution.

TL;DR: It is shown that this approach is generally applicable and significantly increases particle density for a range of samples, such as small protein complexes, viruses and filamentous assemblies, and can enable characterization of samples that would otherwise resist structural studies using single particle cryoEM.

TL;DR: It is shown that YFP and GFP have enhanced blinking properties when embedded in acrylic resin and imaged under partial vacuum, enabling in vacuo single molecule localisation microscopy.

TL;DR: The present study revealed that the disruption in the arrangement of the osteocyte network and collagen/BAp microstructure and the deterioration of mechanical function occurred synchronously during cancer bone metastasis.

TL;DR: This article discusses the recently expanded set of FRET-based tension sensors that allows the analysis of mechanical forces with piconewton sensitivity in cells and provides a theoretical framework for the design of additional tension sensor modules with adjusted force sensitivity.

TL;DR: A convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms and can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.

TL;DR: A set of scoring functions that compare 3D-EM volumes that show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features and a combined score involving the local mutual information and overlap performs best overall.

TL;DR: A microscopic theory for selectins is described, which provides a structural basis for catch bonds and predicts a crucial allosteric role for residues Asn82-Glu88 and the need for new theories and simulations that can mimic experimental conditions is emphasized.

TL;DR: This work presents a comprehensive solution for a 3D CTF correction based on the Jensen-Kornberg scheme, which performs a slice-by-slice correction of the CTF within the tomographic reconstruction and finds that 3DCTF correction always produces equal or better results than 2D C TF correction.

TL;DR: Crystal structures of FtsZ from Staphylococcus aureus corresponding to the T and R state conformations in the same crystal are reported, indicating the structural equilibrium of the two state.

TL;DR: Cryo-SEM data of cells undergoing EV blebbing and shedding is presented here for the first time and suggests a difference in the effects of the two stimulation types on the shedding process and possibly on the type of EVs shed.

TL;DR: The ribosome is the main survivor of this primordial RNA world and offers an excellent model system for retracing the steps that led to the folded proteins of today, due to its very slow rate of change.

TL;DR: It is shown that in situ sub-volume averaging from single tomograms can guide and complement segmentation of biological features, and the in situ determination of the structure of individual viruses is possible as they infect a cell.

TL;DR: This work describes three increasingly sophisticated cantilever modifications that yield enhanced data quality in AFM-based single-molecule force spectroscopy and illustrates how these three metrics are limited by the cantilevers itself rather than the larger microscope structure.

TL;DR: The acquired unique information on 3D plaque fiber direction will help understanding pathobiological mechanisms of atherosclerotic plaque progression and pave the road to more realistic biomechanical plaque modeling for rupture assessment.

TL;DR: The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.