Showing papers in "Journal of Structural Biology in 2015"

TL;DR: Modifications to the CTFFIND algorithm are described which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates.

TL;DR: A fully CTF-corrected template-based picking algorithm is supplemented by a fast sorting algorithm and reference-free 2D class averaging to remove false positives and yields results that are comparable to manual particle selection.

TL;DR: In this paper, an algorithm that allows for individual <1 MDa particle images to be aligned without frame averaging or linear trajectories was proposed, which maximizes the overall correlation of shifted frames with the sum of the shifted frames.

TL;DR: Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures, and demonstrates features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex.

TL;DR: After 3D reconstruction, tomograms acquired with the combination of a VPP and an energy filter showed structural features in neuronal processes with outstanding clarity, and it is expected that VPP will become a standard element of the electron cryotomography workflow.

TL;DR: A technical description and an assessment of the optimizations included in Tomo3D to take advantage of Advanced Vector eXtensions (AVX) instructions are provided.

TL;DR: It is demonstrated that the distortion present on the Titan Krios microscope limits the resolution of a set of rotavirus VP6 images to ∼7 Å, which increases to ∼3 Å following estimation and correction of the distortion.

TL;DR: It is reported that eggshell mineral originates from the accumulation of flat disk-shaped amorphous calcium carbonate particles on specific organic sites on the eggshell membrane, which are rich in proteins and sulfated proteoglycans.

TL;DR: A workflow for preparing lamellas from Caenorhabditis elegans worms using cryo-FIB applied to high pressure frozen samples is described and a dedicated lift-out procedure at cryogenic temperature is developed.

TL;DR: The X-ray crystal structure reveals the binding mode of AZD9291 to the kinase domain of wild type EGFR, which shows a 200-fold selectivity for T790M/L858R over wildtype EGFR.

TL;DR: These structures can provide starting points for the development of antibodies and inhibitory molecules targeting protein-protein interactions, with the aim to inhibit invasion, and discuss recent work regarding alternative models.

TL;DR: A computer-assisted system, named UCSFImage4, for semi-automated cryo-EM image acquisition that implements an asynchronous data acquisition scheme that facilitates efficient acquisition, on-the-fly motion correction, and CTF analysis of dose fractionated image stacks with a total time of ∼60s/exposure.

TL;DR: The EMAN2.1 SPT toolbox is presented, which offers a full SPT processing pipeline, from particle picking to post-alignment analysis of subtomogram averages, automating most steps, providing versatility and allowing for procedural cross-testing and specimen-specific strategies.

TL;DR: A comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2 Å in resolution using cryo-EM.

TL;DR: The Fourier slice theorem is extended to covariance functions showing that the three-dimensional covariance, and hence the principal components, of a heterogeneous particle can indeed be recovered from two-dimensional cryo-EM images.

TL;DR: It is expected that the capability of non-destructive three-dimensional mapping of mass density in biological samples close to their native state becomes a valuable method for measuring the packing of organic matter on the nanoscale.

TL;DR: A set of automated, correlation-based tilt-series alignment, contrast transfer function (CTF) correction, and reconstruction workflows for use in conjunction with the Appion/Leginon package that are primarily targeted at automating structure determination with cryogenic electron microscopy are presented.

TL;DR: The signal formation in the sensor and its impact on the detection quantum efficiency (DQE) of the sensor is described and insights into the signal formation led to improved camera designs.

TL;DR: This work develops a BIM correction method at the image level, resulting in an integrated image in which the in-plane BIM blurring is compensated prior to particle picking.

TL;DR: A new data processing protocol is developed that can accurately determine αβ-tubulin register and seam location for MT segments and visualize the nucleotide state at the E-site and the configuration of lateral contacts at the seam.

TL;DR: A set of extensions to the MRC format standard designed to accommodate variants of the file format, while restoring interoperability with crystallography software are proposed.

TL;DR: Two resin formulations, Hard Plus and the mixture of Durcupan/Epon, emerged that were considerably less affected and reasonably stable in the electron/ion beam and thus suitable for the 3-D investigation of biological samples.

TL;DR: The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry and is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching.

TL;DR: The structural features, determining the different reaction products, to reside in just a few loops at the rim of the active site funnel are proposed and it is proposed that loop 8 may have a role in product length determination in Gluconacetobacter diazotrophicus LsdA and Microbacterium saccharophilum FFase.

TL;DR: Capsid surface differences which can serve as template regions for rational design of vectors with enhanced transduction for specific tissues and escape pre-existing antibody recognition are identified, essential for the creation of an AAV vector toolkit that is amenable to personalized disease treatment.

TL;DR: By analyzing entire mouse islets, serial block-face scanning electron microscopy is applied to measure parameters that describe the architecture of pancreatic islets of Langerhans, microscopic endocrine organs that secrete insulin and glucagon for control of blood glucose.

TL;DR: It is concluded that the filopodial network is an integral part of the mineral transport process, and possibly also for sequestering calcium and other ions.

TL;DR: The 3D nature of the SR μCT data sets furthermore revealed that lacunae in central bone, which appear to be poorly aligned in transverse 2D cross sections, are in fact highly aligned along the bone long axis.

TL;DR: The crystal structure of PE- PPE domains of EspB is determined, which represents an all-helical, elongated molecule closely resembling the structure of the PE25-PPE41 heterodimer despite limited sequence similarity, and provides a rationale for the future investigation of Esp B's role in M. tuberculosis pathogenesis.

TL;DR: X-ray phase contrast tomography is used to resolve the structure of uncut, entire myelinated optic, saphenous and sciatic mouse nerves as well as identification of sub-structures such as nodes of Ranvier and Schmidt-Lanterman incisures.