Abstract：
:The Bsoft package is aimed at processing electron micrographs for the determination of the three-dimensional structures of biological specimens. Recent advances in hardware allow us to solve structures to near atomic resolution using single particle analysis (SPA). The Map Challenge offered me an opportunity to test the ability of Bsoft to produce reconstructions from cryo-electron micrographs at the best resolution. I also wanted to understand what needed to be done to work towards full automation with validation. Here, I present two cases for the Map Challenge using Bsoft: ß-galactosidase and GroEL. I processed two independent subsets in each case with resolution-limited alignment. In both cases the reconstructions approached the expected resolution within a few iterations of alignment. I further validated the results by coherency-testing: i.e., that the reconstructions from real particles give better resolutions than reconstructions from the same number of aligned noise images. The key operations requiring attention for full automation are: particle picking, faster accurate alignment, proper mask generation, appropriate map sharpening, and understanding the amount of data needed to reach a desired resolution.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Heymann JBdoi
10.1016/j.jsb.2018.07.003subject
Has Abstractpub_date
2018-10-01 00:00:00pages
90-95issue
1eissn
1047-8477issn
1095-8657pii
S1047-8477(18)30161-8journal_volume
204pub_type
杂志文章abstract：:The Membrane Attack Complex-Perforin (MACPF) family is ubiquitously found in all kingdoms. They have diverse cellular roles, however MACPFs with pore-forming toxic function in venoms and poisons are very rare in animals. Here we present the structure of PmPV2, a MACPF toxin from the poisonous apple snail eggs, that ca...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107531
更新日期：2020-08-01 00:00:00
abstract：:Gap junctions containing extensive, highly ordered crystalline arrays of hexagonally packed connexons have been isolated from the hepatopancreas of the arthropod, Homarus americanus (American lobster). The structure of such junctions has been studied to a resolution of approximately 25 A in three dimensions by electro...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90075-8
更新日期：1991-06-01 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：:The C1q-tumor necrosis factor 5 (C1QTNF5) protein plays a significant role in retinal pigmented epithelium (RPE) cellular adhesion. The C1QTNF5 gene is co-transcribed with the frizzled-related protein (MFRP) gene. A Ser-to-Arg mutation at site 163 (S163R) in C1QTNF5 is known to cause late-onset retinal macular degener...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.02.001
更新日期：2014-04-01 00:00:00
abstract：:High-resolution light-microscopy and high-throughput screening are two essential methodologies for characterizing cellular phenotypes. Optimally combining these methodologies in cell-based screening to test detailed molecular and cellular responses to multiple perturbations constitutes a major challenge. Here we descr...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.12.013
更新日期：2007-05-01 00:00:00
abstract：:The AAA+ family of proteins play fundamental roles in all three kingdoms of life. It is thought that they act as molecular chaperones in aiding the assembly or disassembly of proteins or protein complexes. Recent structural studies on a number of AAA+ family proteins have revealed that they share similar structural el...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.11.022
更新日期：2004-04-01 00:00:00
abstract：:In fishes, like in amphibians, it is well established that variations in rRNA activity occur during oogenesis. Contrary to amphibians, however, little is known about the ultrastructural changes of the nucleolus during fish oogenesis. Evolution of the nucleolus has been followed during oogenesis in the teleost fish Bar...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.07.006
更新日期：2005-10-01 00:00:00
abstract：:Dipeptidase 3 (DPEP3) is one of three glycosylphosphatidylinositol-anchored metallopeptidases potentially involved in the hydrolytic metabolism of dipeptides. While its exact biological function is not clear, DPEP3 expression is normally limited to testis, but can be elevated in ovarian cancer. Antibody drug conjugate...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107512
更新日期：2020-07-01 00:00:00
abstract：:Mononuclear macrophages are important immune cells in the organisms. The complicated membrane structure underlying the diverse functions of mononuclear-macrophage has been largely unresolved. As a representative of monocyte-derived macrophages, the membrane structure of PMA differentiated THP-1 cells was comprehensive...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2019.04.002
更新日期：2019-06-01 00:00:00
abstract：:This study demonstrates the effects of progesterone on eggshell quality and ultrastructure by injecting progesterone into laying hens 2 and 5 h post-oviposition, respectively. Progesterone injected 2 h post-oviposition (P4-2 h) improved eggshell quality with a significant decrease (P < 0.01) in the thickness of the ma...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2019.107430
更新日期：2020-02-01 00:00:00
abstract：:In situ hybridization (ISH) is a widely applied technique used for visualizing specific nucleic acid sequences at chromosomal, cytologic, and histologic levels. It sometimes fails, however, to demonstrate precise cell identity, early stages of gene expression and variants of alternative splicing because of its limited...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.09.010
更新日期：2006-01-01 00:00:00
abstract：:The recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been characterised and its crystal structure elucidated at 1.85A. The global architecture of the protein is reminiscent of that of the amidohydrolase superfamily, consisting of two domains; an (alpha/beta)(8) TIM-like barrel domain,...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.10.013
更新日期：2010-02-01 00:00:00
abstract：:Processing of nuclear pre-mRNA is an important step in the regulation of gene expression and involves 5(')- and 3(')-end processing, splicing, and editing. Mammalian nuclear pre-mRNAs are assembled in large ribonucleoprotein (lnRNP) complexes, in which the entire population of nuclear pre-mRNA is individually packaged...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/s1047-8477(02)00541-5
更新日期：2002-10-01 00:00:00
abstract：:We have cloned and expressed in Escherichia coli cDNA for rat nuclear transport factor 2 (NTF2), a key cytoplasmic factor that facilitates the import of proteins into the nucleus through nuclear pores. We have used this bacterially expressed material to produce orthorhombic crystals suitable for high-resolution X-ray ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1996.0049
更新日期：1996-03-01 00:00:00
abstract：:While cryo-electron tomography (cryo-ET) can reveal biological structures in their native state within the cellular environment, it requires the production of high-quality frozen-hydrated sections that are thinner than 300nm. Sample requirements are even more stringent for the visualization of membrane-bound protein c...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.07.010
更新日期：2017-02-01 00:00:00
abstract：:In bacteria, the two-component system (TCS) is the most prevalent for sensing and transducing the environmental signals into the cell. In Salmonella, the small basic protein PmrD is found to protect phospho-PmrA and prolong the expression of PmrA-activated genes. In contrast, Escherichia coli PmrD fails to protect pho...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.06.007
更新日期：2010-12-01 00:00:00
abstract：:Sialic acid residues found as terminal monosaccharides in various types of glycan chains in cell surface glycoproteins and glycolipids have been identified as important contributors of cell-cell interactions in normal vs. abnormal cellular behavior and are pivotal in diseases such as cancers. In vertebrates, sialic ac...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107628
更新日期：2020-11-01 00:00:00
abstract：:The repetitive Gly-X-Y sequence is the telltale sign of triple helical domains in collagens and collagen-like proteins. Most collagen sequences contain sporadic interruptions of this pattern, which may have functional roles in molecular flexibility, assembly or molecular recognition. However, the structural signatures...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.03.022
更新日期：2014-06-01 00:00:00
abstract：:The morphology and structure of giant starch granules from the pseudo-bulbs of Phajus grandifolius were investigated, using a number of microscopy techniques together with synchrotron radiation microdiffration analysis. Most of the granules, which had sizes between 100 and 200 microm, occurred as ogival particles with...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.11.007
更新日期：2006-04-01 00:00:00
abstract：:HIV-1 Rev mediates the nuclear export of unspliced and partially-spliced viral transcripts for the production of progeny genomes and structural proteins. In this process, four (or more) copies of Rev assemble onto a highly-structured 351-nt region in such viral transcripts, the Rev response element (RRE). How this occ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.03.011
更新日期：2018-08-01 00:00:00
abstract：:Structures of biological macromolecules determined by transmission cryoelectron microscopy (cryo-TEM) and three-dimensional image reconstruction are often displayed as surface-shaded representations with depth cueing along the viewed direction (Z cueing). Depth cueing to indicate distance from the center of virus part...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1997.3902
更新日期：1997-10-01 00:00:00
abstract：:In order to successfully perform the 3D reconstruction in electron tomography, transmission electron microscope images must be accurately aligned or registered. So far, the problem is solved by either manually showing the corresponding fiducial markers from the set of images or automatically using simple correlation b...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2001.4343
更新日期：2001-01-01 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：:Neuropeptide gamma (NPgamma) is a neurokinin-2 (NK-2) receptor selective agonist, which plays an important role in mediation of asthma and elicits a wide range of biological responses like bronchoconstriction, vasodepression and regulation of endocrine functions. The structure determination of this peptide agonist is ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2004.08.008
更新日期：2004-12-01 00:00:00
abstract：:The Omp21 protein from the proteobacterium Comamonas (Delftia) acidovorans belongs to the recently described beta8 family of outer membrane proteins, characterized by eight antiparallel beta-strands which form a beta-barrel. This family includes virulence proteins, OmpA and OmpX from Escherichia coli, and other relate...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2000.4261
更新日期：2000-08-01 00:00:00
abstract：:Cystathionine β-synthase (CBS) domains are small intracellular modules that can act as binding domains for adenosine derivatives, and they may regulate the activity of associated enzymes or other functional domains. Among these, the single CBS domain-containing proteins, CBSXs, from Arabidopsis thaliana, have recently...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2013.04.013
更新日期：2013-07-01 00:00:00
abstract：:The AAA family proteins usually form a hexameric ring structure. The ATP-binding pocket, which is located at the interface of subunits in the hexamer, consists of three functionally important motifs, the Walker A and B motifs, and the second region of homology (SRH). It is well known that Walker A and B motifs mediate...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.03.001
更新日期：2006-10-01 00:00:00
abstract：:The structure of the smooth muscle contractile apparatus was studied using ultrarapid freezing followed by freeze substitution or by longitudinal freeze-fracture, deep-etch, and platinum-carbon replication. Freeze substitution minimises the detrimental effects of chemical fixation and freeze fracture eliminates them e...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1995.1009
更新日期：1995-03-01 00:00:00
abstract：:CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm whi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2015.08.008
更新日期：2015-11-01 00:00:00
abstract：:Calnexin is a molecular chaperone that facilitates folding of glycoproteins in the endoplasmic reticulum (ER). The cloned lumenal domain of canine calnexin, cnxDeltaTMC, retains its biological activity without the transmembrane and cytosolic region. For the purpose of structure determination we generated a crystalliza...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.4032
更新日期：1998-11-01 00:00:00
