Abstract:
:In COPII mediated vesicle formation, Sec13/Sec31 heterotetramers play a role in organizing the membranes into a spherical vesicle. There they oligomerize into a cage that interacts with the other COPII proteins to direct vesicle formation and concentrate cargo into a bud. In this role they must be flexible to accommodate different sizes and shapes of cargo, but also have elements that provide rigidity to help deform the membrane. Here we characterize the influence the C-terminal disordered region of Sec31 has on cage flexibility and rigidity. After deleting this region (residues 820-1220), we characterized Sec13/Sec31ΔC heterotetramers biophysically and structurally through cryo-EM. Our results show that Sec13/31ΔC self-assembles into canonical cuboctahedral cages in vitro at buffer conditions similar to wild type. The distribution of cage sizes indicated that unlike the wild type, Sec13/31ΔC cages have a more homogeneous geometry. However, the structure of cuboctahedrons exhibited more conformational heterogeneity than wild type. Through localized reconstruction of cage vertices and molecular dynamics flexible fitting we found a new hinge for the flexing of Sec31 β-propeller domain and more flexibility of the previously known hinge. Together, these results show that the C-terminal region of Sec31 regulates the flexing of other domains such that flexibility and rigidity are not compromised during transport of large and/or asymmetric cargo.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Paraan M,Bhattacharya N,Uversky VN,Stagg SMdoi
10.1016/j.jsb.2018.08.016subject
Has Abstractpub_date
2018-11-01 00:00:00pages
250-260issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(18)30247-8journal_volume
204pub_type
杂志文章abstract::Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to stu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2014.04.006
更新日期:2014-07-01 00:00:00
abstract::3,4-dihydroxy 2-butanone 4-phosphate synthase (DHBPS) and GTP cyclohydrolase-II (GTPCH-II) are the two initial enzymes involved in riboflavin biosynthesis pathway, which has been shown to be essential for the pathogens. In Mycobacterium tuberculosis (Mtb), the ribA2 gene (Rv1415) encodes for the bi-functional enzyme w...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.01.013
更新日期:2011-05-01 00:00:00
abstract::Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte-Carlo type of optimization algorithm, for globally aligning the center and orientation of a particle simultaneously. A consistency crite...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.06.009
更新日期:2007-10-01 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::Single-axis cryo-electron tomography of vitrified specimens has become a method of choice to reconstruct in three dimensions macromolecular assemblies in their cellular context or prepared from purified components. Here, we asked how a dual-axis acquisition scheme would improve three-dimensional reconstructions of mic...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.11.004
更新日期:2013-02-01 00:00:00
abstract::MDPP is a fully featured general-purpose image processing package primarily written to support research in structural biology using data gathered by electron microscopy. It has focused on the analysis of images using Fourier techniques, particularly periodic plane-layer and helical structures, but has extensive tools ...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1006/jsbi.1996.0007
更新日期:1996-01-01 00:00:00
abstract::DNA-dependent protein kinase (DNA-PK) is part of the eukaryotic DNA double strand break repair pathway and as such is crucial for maintenance of genomic stability, as well as for V(D)J (variable-diversity-joining) recombination. The catalytic subunit of DNA-PK (DNA-PKcs) belongs to the phosphatidylinositol-3 (PI-3) ki...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2003.11.024
更新日期:2004-03-01 00:00:00
abstract::Computational modeling of membrane proteins is critical to understand biochemical systems and to support chemical biology. In this work, we use a dataset of 448 non-redundant membrane protein chains to expose a "rule" that governs membrane protein structure: free cysteine thiols are not found accessible to oxidative c...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2019.10.002
更新日期:2020-01-01 00:00:00
abstract::Riboflavin synthase is a trimer of identical 23-kDa subunits. The primary structure is characterized by considerable similarity of the C-terminal and N-terminal parts. Recombinant riboflavin synthase of Escherichia coli and Bacillus subtilis was crystallized by the vapor diffusion method. Crystals of E. coli riboflavi...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1997.3935
更新日期:1998-01-01 00:00:00
abstract::Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of d-fructose to d-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mecha...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.05.007
更新日期:2010-09-01 00:00:00
abstract::This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.02.005
更新日期:2013-02-18 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::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
更新日期:2008-03-01 00:00:00
abstract::Sequence comparisons have been undertaken for all hair and epithelial keratin IF chains from a single species--human. The results lead to several new proposals. First, it is clear that not only is the chain structure of the molecule an obligate heterodimer but promiscuous association of Type I and Type II chains must ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.12.002
更新日期:2007-06-01 00:00:00
abstract::BCP1 is a protein enriched in the nucleus that is required for Mss4 nuclear export and identified as the chaperone of ribosomal protein Rpl23 in Saccharomyces cerevisiae. According to sequence homology, BCP1 is related to the mammalian BRCA2-interacting protein BCCIP and belongs to the BCIP protein family (PF13862) in...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107605
更新日期:2020-10-01 00:00:00
abstract::Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at approximately 30nm resolution. Here, we report the first a...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2009.02.014
更新日期:2009-06-01 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::Amyloid formation is associated with a range of debilitating human disorders including Alzheimer's and prion diseases. The amyloid structure is essential for understanding the role of amyloids in these diseases. Amyloid formation of Ure2 protein underlies the yeast prion [URE3]. Here we use site-directed spin labeling...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.08.008
更新日期:2012-11-01 00:00:00
abstract::Chaperonins mediate protein folding in an ATP-dependent manner. ATP binding and hydrolysis by chaperonins are subject to both homotropic and heterotropic allosteric regulation. In the case of GroEL and CCT, homotropic regulation by ATP is manifested in nested cooperativity, which involves positive intra-ring cooperati...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1006/jsbi.2001.4377
更新日期:2001-08-01 00:00:00
abstract::DivIVA or Wag31, which is an essential pole organizing protein in mycobacteria, can self-assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. The structu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2019.107429
更新日期:2020-02-01 00:00:00
abstract::Folding and self-assembly of amyloid beta (Abeta) peptide are linked to Alzheimer's disease. To understand the initial stage of amyloid-beta peptide aggregation, conformational characteristics of monomers of wild-type (WT) Abeta(28-35) and its mutant peptides A30G and A30I were investigated using density functional th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.02.017
更新日期:2010-06-01 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::Lateral pressure profiles have been suggested to play a significant role in many cellular membrane processes by affecting, for example, the activation of membrane proteins through changes in their conformational state. This may be the case if the lateral pressure profile is altered due to changes in molecular composit...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.01.012
更新日期:2007-08-01 00:00:00
abstract::Single crystals of UDP-N-acetylglucosamine enolpyruvyltransferase of Enterobacter cloacae have been grown by vapor diffusion using phosphate buffer as the precipitant. The crystals belong to the monoclinic space group C2 with a = 86.9 A, b = 155.9 A, c = 83.8 A, beta = 91.6 degrees. Assuming two monomers per asymmetri...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1996.0071
更新日期:1996-07-01 00:00:00
abstract::A defining property of a crystal is its symmetry. This mini-review sets out to summarize all aspects that define 2D crystallographic symmetry as applied to the study of macromolecular structure. It begins by defining molecular point symmetries, before covering crystallographic symmetry operations in 2D, common notatio...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.jsb.2007.07.002
更新日期:2007-12-01 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
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.04.003
更新日期:2010-07-01 00:00:00
abstract::When biological macromolecules are imaged in the transmission electron microscope (TEM), their inherent handedness is lost because the three-dimensional (3D) structure is projected onto a two-dimensional (2D) plane, and identical 2D projections can be made from either 3D enantiomer. Nevertheless, tilt experiments in t...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1997.3896
更新日期:1997-10-01 00:00:00
abstract::The structure and motility of the Mollicutes (Spiroplasma, Mycoplasma, and Acholeplasma) are briefly reviewed. The data are presented from the perspective of prokaryotic and eukaryotic motors, cytoskeletons, and cell motility. The Mollicutes are eubacteria derived from Clostridia by regressive evolution and genome red...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1006/jsbi.1998.4063
更新日期:1998-12-15 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 rod domain of IF molecules has been characterized as four alpha-helical coiled-coil segments (1A, 1B, 2A and 2B), three linkers (L1, L12 and L2) and a stutter at the centre of segment 2B. Two of these breaks in coiled-coil continuity (L2 and stutter) have been modelled on the basis of structural data obtained from...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2009.12.006
更新日期:2010-05-01 00:00:00