Abstract：
:The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Demo G,Papoušková V,Komárek J,Kadeřávek P,Otrusinová O,Srb P,Rabatinová A,Krásný L,Žídek L,Sklenář V,Wimmerová Mdoi
10.1016/j.jsb.2014.06.001subject
Has Abstractpub_date
2014-08-01 00:00:00pages
174-186issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(14)00137-3journal_volume
187pub_type
杂志文章abstract：:Cryo-electron microscopy (cryo-EM) of frozen-hydrated preparations of isolated macromolecular complexes is the method of choice to obtain the structure of complexes that cannot be easily studied by other experimental methods due to their flexibility or large size. An increasing number of macromolecular structures are ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.04.007
更新日期：2016-06-01 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...
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pub_type： 杂志文章
doi：10.1016/j.jsb.2016.09.009
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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
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abstract：:Anti-TRAP (AT) protein regulates expression of tryptophan biosynthetic genes by binding to the trp RNA-binding attenuation protein (TRAP) and preventing its interaction with RNA. Bacillus subtilis AT forms trimers that can either interact with TRAP or can further assemble into dodecameric particles. To determine which...
journal_title：Journal of structural biology
pub_type： 杂志文章
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更新日期：2010-04-01 00:00:00
abstract：:We have developed a simplified, efficient approach for the 3D reconstruction and analysis of mammalian cells in toto by electron microscope tomography (ET), to provide quantitative information regarding 'global' cellular organization at approximately 15-20 nm resolution. Two insulin-secreting beta cells-deemed 'functi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.09.015
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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
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journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2000.4211
更新日期：2000-05-01 00:00:00
abstract：:Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavor...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.08.005
更新日期：2016-12-01 00:00:00
abstract：:Ferritin, the major iron storage protein, has dual functions; it sequesters redox activity of intracellular iron and facilitates iron turn-over. Here we present high angle annular dark field (HAADF) images from individual hepatic ferritin cores within tissue sections, these images were obtained using spherical aberrat...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.12.001
更新日期：2009-04-01 00:00:00
abstract：:Cryoelectron microscopy makes it possible to record high-resolution detail from large and complex structures. However, its application to understanding cellular structure is limited by the requirement that samples should be no thicker than approximately 0.5-1 microm. Therefore it is important to develop the ability to...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/s1047-8477(03)00016-9
更新日期：2003-05-01 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：:Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the differen...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.04.001
更新日期：2016-07-01 00:00:00
abstract：:Recent advances in cryo-electron tomography (cryo-ET) have allowed direct visualization of the initial interactions between bacteriophages and their hosts. Previous studies focused on phage infection in Gram-negative bacteria but it is of particular interest how phages penetrate the thick, highly cross-linked Gram-pos...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.07.019
更新日期：2017-02-01 00:00:00
abstract：:Water-containing biological material cannot withstand the vacuum of the transmission electron microscope. The classical solution to this problem has been to dehydrate chemically fixed biological samples and then embed them in resin. During such treatment, the bacterial nucleoid is especially prone to aggregation, whic...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.jsb.2006.07.007
更新日期：2006-11-01 00:00:00
abstract：:A topological localization of epitopes on the surface of the Aa6 subunit of Androctonus australis hemocyanin has been carried out. First, immunocomplex strings composed of native hemocyanin and monoclonal antibodies were examined in the electron microscope and submitted to an image processing by correspondence analysi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(90)90087-s
更新日期：1990-03-01 00:00:00
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journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.jsb.2003.10.009
更新日期：2004-04-01 00:00:00
abstract：:The genomic DNA in cells of Escherichia coli is localized in one or two compact, phase-like regions with characteristic shapes. Nucleoids undergo progressive changes in shape and compaction in the presence of drugs such as chloramphenicol or puromycin. Forces which influence nucleoid shape and compaction are reviewed,...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.jsb.2006.03.022
更新日期：2006-11-01 00:00:00
abstract：:Native troponin-tropomyosin complex was isolated from Lethocerus indicus indirect flight muscle and tested for function. It was shown by rotary shadowing and by forming paracrystals on monolayers that the regulatory complex consists of a troponin head region approximately 130 A in diameter and a 400-A-long troponin T-...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1996.3834
更新日期：1997-02-01 00:00:00
abstract：:Tobacco streak virus (TSV), the type member of Ilarvirus genus, is a major plant pathogen. TSV purified from infected plants consists of a ss-RNA genome encapsidated in spheroidal particles with diameters of 27, 30 and 33nm constructed from multiple copies of a single species of coat protein (CP) subunits. Apart from ...
journal_title：Journal of structural biology
pub_type： 杂志文章
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更新日期：2016-02-01 00:00:00
abstract：:Bdelloid rotifers are aquatic microinvertebrates able to cope with the loss of environmental water by entering dormancy, and are thus capable of living in temporary habitats. When water is evaporating, bdelloids contract into "tuns", silence metabolism and lose water from the body, a condition known as anhydrobiosis. ...
journal_title：Journal of structural biology
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doi：10.1016/j.jsb.2010.04.003
更新日期：2010-07-01 00:00:00
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journal_title：Journal of structural biology
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doi：10.1016/j.jsb.2009.10.013
更新日期：2010-02-01 00:00:00
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journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.02.007
更新日期：2011-05-01 00:00:00
abstract：:Insect flight muscle (IFM) can oscillate at frequencies up to 1000Hz, owing to its capability of stretch activation (SA). It is a highly specialized form of cross striated muscles, and its peculiar features include the IFM-specific isoform of troponin-I (troponin-H or TnH) with an unusually long Pro-Ala-rich extension...
journal_title：Journal of structural biology
pub_type： 杂志文章
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更新日期：2013-07-01 00:00:00
abstract：:The mature dentinoenamel junction (DEJ) is viewed by some investigators and the current authors, not as a fossilized, sharp transition between enamel and dentin, but as a relatively broad structural transition zone including the mantle dentin and the inner aprismatic enamel. In this study, the DEJ structure in bovine ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.10.006
更新日期：2008-02-01 00:00:00
abstract：:This study probes the early events during lag phase of aggregation of GNNQQNY using all atom MD simulations in explicit solvent. Simulations were performed by varying system size, temperature and starting configuration. Peptides dispersed randomly in the simulation box come together early on in the simulation and form...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2015.09.020
更新日期：2015-12-01 00:00:00
abstract：:Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE softwa...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.08.005
更新日期：2018-11-01 00:00:00
abstract：:By taking advantage of network-based computing and the recent developments in Web interfaces, centralized research facilities housing specialized and unique imaging instruments along with associated high-performance computing can be made available to researchers for use from their own laboratories. In addition to incr...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
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更新日期：1999-04-01 00:00:00
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journal_title：Journal of structural biology
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更新日期：2016-06-01 00:00:00
abstract：:Trypanosoma cruzi chagasin belongs to a recently discovered family of cysteine protease inhibitors found in lower eukaryotes and prokaryotes but not in mammals. Chagasin binds tightly to cruzain, the major lysosomal T. cruzi cysteine protease, involved with infectivity and survival of the parasite in mammalian host ce...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.07.017
更新日期：2007-02-01 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
