Abstract:
:We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
He S,Scheres SHWdoi
10.1016/j.jsb.2017.02.003subject
Has Abstractpub_date
2017-06-01 00:00:00pages
163-176issue
3eissn
1047-8477issn
1095-8657pii
S1047-8477(17)30019-9journal_volume
198pub_type
杂志文章abstract::Lichens are symbiotic associations of fungi and algae (or cyanobacteria). Fungal cells produce large amounts of lipid, assisted by algae, and secrete them out of the cells. Some of the secreted lipids crystallize in the thallus of the lichen. The crystalline materials sometimes occupy 30% of total dry weight of the th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2004.01.015
更新日期:2004-06-01 00:00:00
abstract::We describe novel structural domains in in vitro reconstituted Xenopus sperm nuclei, which we term RPA bodies; RPA is the only known marker of these structures. These bodies contain DNA and represent special chromatin domains as seen by transmission electron microscopy. We show that RPA bodies exhibit a similar ultras...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2000.4229
更新日期:2000-04-01 00:00:00
abstract::Ribonucleic acids (RNAs) play a key role in many fundamental life processes. These polymers are often found complexed with proteins in extremely large particles whose molecular mass may reach several millions of daltons (e.g., ribosomes, spliceosomes, and viruses). Structural studies of such RNA-protein complexes shou...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1999.4134
更新日期:1999-09-01 00:00:00
abstract::The β-carbonic anhydrases (β-CAs) are widely distributed zinc-metalloenzymes that play essential roles in growth, survival, development and virulence in fungi. The majority of filamentous ascomycetes possess multiple β-CA isoforms among which major and minor forms have been characterized. We examined the catalytic beh...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2019.07.011
更新日期:2019-10-01 00:00:00
abstract::Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and stru...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.12.004
更新日期:2013-03-01 00:00:00
abstract::Here we report the first crystal structure of a secretory α-glucoside hydrolase isolated from Pseudoalteromonas sp. K8, PspAG97A, which belongs to glycoside hydrolase family 97 and exhibits halophilic property. PspAG97A lacks an acidic surface, that is considered essential for protein stability at high salinity. Inter...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.09.009
更新日期:2016-12-01 00:00:00
abstract::We describe here a set of multiresolution visualization and docking procedures that we refer to as the Situs package. The package was developed to provide an efficient and robust method for the fitting of atomic structures into low-resolution data. The current release was optimized specifically for the visualization a...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2000.4350
更新日期:2001-02-01 00:00:00
abstract::A characteristic feature of the dense phases formed by fiber-shaped molecules is their organization into parallel rods packed in a hexagonal or pseudo-hexagonal lateral network. This is typically the case for the collagen triple helices inside fibrils, as confirmed by recent X-ray diffraction experiments carried out o...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.11.018
更新日期:2011-02-01 00:00:00
abstract::The human vertebral body and intervertebral disc interface forms the region where the cartilaginous endplate, annulus fibrosis and bone of the vertebral body are connected through an intermediate calcified cartilage layer. While properties of both the vertebral body and components of the disc have been extensively stu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.08.011
更新日期:2013-11-01 00:00:00
abstract::Three-dimensional reconstruction of large macromolecules like viruses at resolutions below 10 A requires a large set of projection images. Several automatic and semi-automatic particle detection algorithms have been developed along the years. Here we present a general technique designed to automatically identify the p...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2003.11.028
更新日期:2004-01-01 00:00:00
abstract::The emergence of electron tomography as a tool for three dimensional structure determination of cells and tissues has brought its own challenges for the preparation of thick sections. High pressure freezing in combination with freeze substitution provides the best method for obtaining the largest volume of well-preser...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.09.002
更新日期:2008-03-01 00:00:00
abstract::Light microscopy (LM) approaches are commonly used to attain a description of the cell structure. Even though LM, if compared to electron microscopy (EM), represents a very fast approach, its resolution is, in principle, much lower than in the case of EM. To improve the LM resolution, computational methods based on re...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00574-9
更新日期:2002-10-01 00:00:00
abstract::Understanding skeletal aging and predicting fracture risk is increasingly important with a growing elderly population. We hypothesized that when categorized by external bone size, the male femoral diaphysis would show different strength-age trajectories which can be explained by changes in morphology, composition and ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107650
更新日期:2020-12-01 00:00:00
abstract::The goal of this study is to evaluate the performance of software for automated particle-boxing, and in particular the performance of a new tool (TextonSVM) that recognizes the characteristic texture of particles of interest. As part of a high-throughput protocol, we use human editing that is based solely on class-ave...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.05.017
更新日期:2011-09-01 00:00:00
abstract::Here we introduce plusTipTracker, a Matlab-based open source software package that combines automated tracking, data analysis, and visualization tools for movies of fluorescently-labeled microtubule (MT) plus end binding proteins (+TIPs). Although +TIPs mark only phases of MT growth, the plusTipTracker software allows...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.07.009
更新日期:2011-11-01 00:00:00
abstract::Molecular genetic studies with prokaryotic microorganisms reveal that many different molecular processes contribute to the formation of spontaneous mutations. Besides infidelities in DNA replication and the consequences of environmental mutagens, enzyme-mediated DNA rearrangements bring about important, evolutionarily...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1016/1047-8477(90)90064-j
更新日期:1990-07-01 00:00:00
abstract::Crustaceans form clots by the rapid crosslinking of a hemolymph clottable protein (CP) to form long, branched polymers. Clotting limits hemolymph loss from wounds as well as playing a part in the innate immune response. CP is a 420 kDa homodimer with a large quantity of associated lipid, primarily the carotenoid pigme...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2005.06.008
更新日期:2005-09-01 00:00:00
abstract::Collagen is the most important structural protein of the animal body. Its unique triple-helix structure and extremely high level of crystallinity make it exceptionally efficient in generating the second harmonic of incident light, and we show here how this leads to a novel mode of microscopy of immediate practical sig...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00576-2
更新日期:2003-01-01 00:00:00
abstract::A Gatan 1024 x 1024 slow-scan charge-coupled device (CCD) camera has been interfaced to a JEOL4000EX electron cryomicroscope and explored for its usefulness in the electron crystallographic analysis of thin, glucose-embedded crystals of crotoxin complex kept at -125 degrees C. We show that the camera allows for an on-...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1994.1029
更新日期:1994-07-01 00:00:00
abstract::Three-dimensional crystals were obtained for the membrane domain of the human erythrocyte anion exchanger (AE1, Band 3). Protein homogeneity and stability and the delicate balance between the detergent used and the amount of phospholipids copurifying are critical to the formation of three-dimensional crystals of the A...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00010-2
更新日期:2002-03-01 00:00:00
abstract::To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysacchari...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.05.011
更新日期:2018-09-01 00:00:00
abstract::As a major player of the innate immune system, surfactant protein D (SP-D) recognizes and promotes elimination of various pathogens such as Gram-negative bacteria. SP-D binds to l-glycero-d-manno-heptose (Hep), a constituent of the partially conserved lipopolysaccharide (LPS) inner core of many Gram-negative bacteria....
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.06.019
更新日期:2016-09-01 00:00:00
abstract::Human alpha 2-macroglobulin (alpha 2M), a large tetrameric plasma glycoprotein, inhibits a wide spectrum of proteinases by a particular "trapping" mechanism resulting from the proteolysis of peptide bonds at specific "bait" regions. This induces the hydrolysis of four thiol esters triggering both the possible covalent...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(91)90060-a
更新日期:1991-02-01 00:00:00
abstract::Three-dimensional (3D) electron microscopy (EM) has become a major player in structural cell biology as it enables the analysis of subcellular architecture at an unprecedented level of detail. Interpretation of the resulting 3D volumes strongly depends on segmentation, which consists in decomposing the volume into the...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.10.002
更新日期:2013-01-01 00:00:00
abstract::The KdpFABC complex (Kdp) functions as a K+ pump in Escherichia coli and is a member of the family of P-type ATPases. Unlike other family members, Kdp has a unique oligomeric composition and is notable for segregating K+ transport and ATP hydrolysis onto separate subunits (KdpA and KdpB, respectively). We have produce...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.09.006
更新日期:2008-03-01 00:00:00
abstract::The ability to convert into amyloid fibrils is a common feature of prion proteins. However, not all amyloid-forming proteins act as prions. Here, we compared two homologs of the yeast prion protein Ure2 from Saccharomyces cerevisiae and Saccharomyces paradoxus, ScUre2p and SpUre2p, which have different prion propensit...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.03.008
更新日期:2011-06-01 00:00:00
abstract::Using a 400-kV cryoelectron microscope, we have obtained tomographic reconstructions of frozen-hydrated sea urchin axonemes with 8-10-nm resolution, as assessed by detection of characteristic components including doublet microtubules, radial spokes, central sheath projections, and outer dynein arms. We did not detect ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00020-5
更新日期:2002-04-01 00:00:00
abstract::Zn-alpha2-glycoprotein (ZAG) is a 41 kDa soluble protein that is present in most bodily fluids. The previously reported 2.8 A crystal structure of ZAG isolated from human serum demonstrated the structural similarity between ZAG and class I major histocompatibility complex (MHC) molecules and revealed a non-peptidic li...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2004.04.009
更新日期:2004-11-01 00:00:00
abstract::Gly missense mutations in type I collagen, which replace a conserved Gly in the repeating (Gly-Xaa-Yaa)n sequence with a larger residue, are known to cause Osteogenesis Imperfecta (OI). The clinical consequences of such mutations range from mild to lethal, with more serious clinical severity associated with larger Gly...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.05.003
更新日期:2018-09-01 00:00:00
abstract::Trypsin treatment of staphylococcal alpha-toxin cleaves the molecule into two roughly equally sized parts, which results in inactivation of the toxin. Tetragonal arrays of oligomers, closely resembling the native ones, can however be formed on lipid layers. From tilted views of negatively stained crystals a 3D structu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(92)90024-5
更新日期:1992-05-01 00:00:00