Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Overexpression, purification and preliminary crystallographic analysis of human M-ficolin fibrinogen-like domain.

ABSTRACT: Ficolins, which are comprised of a collagen-like domain and a fibrinogen-like domain, are a kind of pattern-recognition molecule for pathogens in the innate immunity system. To investigate the molecular mechanism of the discrimination between self and non-self by ficolins, human M-ficolin fibrinogen-like domain (FD1), which contains the ligand-binding site, was overexpressed in Pichia pastoris, purified and crystallized using the vapour-diffusion method at 293 K. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 55.16, b = 117.45, c = 55.19 angstroms, beta = 99.88 degrees, and contain three molecules per asymmetric unit. An X-ray data set was collected to 1.9 angstroms resolution using synchrotron radiation at beamline BL24XU at the SPring-8 facility in Japan.

SUBMITTER: Tanio M

PROVIDER: S-EPMC2242945 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Overexpression, purification and preliminary crystallographic analysis of human M-ficolin fibrinogen-like domain.

Tanio Michikazu M Kondo Shin S Sugio Shigetoshi S Kohno Toshiyuki T

Acta crystallographica. Section F, Structural biology and crystallization communications 20060610 Pt 7

Ficolins, which are comprised of a collagen-like domain and a fibrinogen-like domain, are a kind of pattern-recognition molecule for pathogens in the innate immunity system. To investigate the molecular mechanism of the discrimination between self and non-self by ficolins, human M-ficolin fibrinogen-like domain (FD1), which contains the ligand-binding site, was overexpressed in Pichia pastoris, purified and crystallized using the vapour-diffusion method at 293 K. The crystals belong to the monoc ...[more]

PMID: 16820685

Similar Datasets

Overproduction, purification and preliminary crystallographic analysis of the carbohydrate-recognition domain of human langerin.

Project description:Langerin, a lectin that is specific to Langerhans cells, interacts with glycoconjugates through its carbohydrate-recognition domain (CRD). This carbohydrate binding occurs by an avidity-based mechanism that is enabled by the neck domain responsible for trimerization. Langerin binds HIV through its CRD and thus plays a protective role against its propagation by the internalization of virions in Birbeck granules. Here, the overproduction, purification and crystallization of the langerin CRD is reported. Crystals obtained by the hanging-drop vapour-diffusion method allowed the collection of a complete data set to 1.5 A resolution and belonged to the tetragonal space group P4(2), with unit-cell parameters a = b = 79.55, c = 90.14 A.

| S-EPMC2374187 | biostudies-literature

The coiled-coil domain of glycosomal membrane-associated Leishmania donovani PEX14: cloning, overexpression, purification and preliminary crystallographic analysis.

Project description:The glycosomal membrane-associated Leishmania donovani protein PEX14, which plays a crucial role in protein import from the cytosol to the glycosomal matrix, consists of three domains: an N-terminal domain where the signalling molecule binds, a transmembrane domain and an 84-residue coiled-coil domain (CC) that is responsible for oligomerization. CCs are versatile domains that participate in a variety of functions including supramolecular assembly, cellular signalling and transport. Recombinant PEX14 CC was cloned, overexpressed, affinity-purified with in-column thrombin cleavage and further purified by size-exclusion chromatography. Crystals that diffracted to 1.98 Å resolution were obtained from a condition consisting of 1.4 M sodium citrate tribasic dihydrate, 0.1 M HEPES buffer pH 7.5. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 143.98, b = 32.62, c = 95.62 Å, β = 94.68°. Structure determination and characterization are in progress.

| S-EPMC7531246 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of human cystathionine ?-synthase.

Project description:Human cystathionine ?-synthase (CBS) is a pyridoxal-5'-phosphate-dependent hemeprotein, whose catalytic activity is regulated by S-adenosylmethionine. CBS catalyzes the ?-replacement reaction of homocysteine (Hcy) with serine to yield cystathionine. CBS is a key regulator of plasma levels of the thrombogenic Hcy and deficiency in CBS is the single most common cause of homocystinuria, an inherited metabolic disorder of sulfur amino acids. The properties of CBS enzymes, such as domain organization, oligomerization degree or regulatory mechanisms, are not conserved across the eukaryotes. The current body of knowledge is insufficient to understand these differences and their impact on CBS function and physiology. To overcome this deficiency, we have addressed the crystallization and preliminary crystallographic analysis of a protein construct (hCBS516-525) that contains the full-length CBS from Homo sapiens (hCBS) and just lacks amino-acid residues 516-525, which are located in a disordered loop. The human enzyme yielded crystals belonging to space group I222, with unit-cell parameters a=124.98, b=136.33, c=169.83?Å and diffracting X-rays to a resolution of 3.0?Å. The crystal structure appears to contain two molecules in the asymmetric unit which presumably correspond to a dimeric form of the enzyme.

| S-EPMC3515372 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of the globular domain of the human type V myosin Myo5a.

Project description:Type V myosins constitute the main cargo-transporting class of myosin motors in higher eukaryotes. They are mainly defined by their C-terminal globular domain, which is required for cargo binding as well as for motor auto-inhibition in the absence of cargo. To date, high-resolution structures only exist for globular domains from yeast. Since the majority of cellular cargoes in yeast are very different from the cargoes in higher eukaryotes, structural insights into the domain organization of globular domains from human type V myosins are important. The globular domain of human Myo5a was cloned, expressed and crystallized and data sets were collected. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 75.04, b = 86.70, c = 131.41 Å, α = β = γ = 90°, and diffracted with data-collection quality to 2.5 Å resolution.

| S-EPMC3818037 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic analysis of a central domain of human splicing factor 1.

Project description:Pre-mRNA splicing is an essential source of genetic diversity in eukaryotic organisms. In the early stages of splicing, splicing factor 1 (SF1) recognizes the pre-mRNA splice site as a complex with its partner, U2 auxiliary factor 65 kDa subunit (U2AF(65)). A central `mystery' domain of SF1 (SF1md) lacks detectable homology with known structures, yet is the region of highest phylogenetic sequence conservation among SF1 homologues. Here, steps towards determining the SF1md structure are described. Firstly, SF1md was expressed and purified. The presence of regular secondary structure was verified using circular dichroism spectroscopy and the SF1md protein was then crystallized. A native data set was collected and processed to 2.5 Å resolution. The SF1md crystals belonged to space group C2 and have most probable solvent contents of 64, 52 or 39% with three, four or five molecules per asymmetric unit, respectively. Mutually perpendicular peaks on the κ = 180° section of the self-rotation function support the presence of four molecules in the asymmetric unit.

| S-EPMC3080157 | biostudies-literature

Overexpression, purification, crystallization and preliminary X-ray crystallographic analysis of the periplasmic domain of outer membrane protein A from Acinetobacter baumannii.

Project description:Outer membrane protein A from Acinetobacter baumannii (AbOmpA) is a major outer membrane protein and a key player in the bacterial pathogenesis that induces host cell death. AbOmpA is presumed to consist of an N-terminal ?-barrel transmembrane domain and a C-terminal periplasmic OmpA-like domain. In this study, the recombinant C-terminal periplasmic domain of AbOmpA was overexpressed in Escherichia coli, purified and crystallized using the vapour-diffusion method. A native diffraction data set was collected to a resolution of 2.0 Å using synchrotron radiation. The space group of the crystal was P2(1), with unit-cell parameters a = 58.24, b = 98.59, c = 97.96 Å, ? = 105.92°. The native crystal contained seven or eight molecules per asymmetric unit and had a calculated Matthews coefficient of 2.93 or 2.56 Å(3) Da(-1).

| S-EPMC3232131 | biostudies-literature

Purification, crystallization and preliminary crystallographic characterization of the caspase-recruitment domain of human Nod1.

Project description:The caspase-recruitment domain (CARD) is known to play an important role in apoptosis and inflammation as an essential protein-protein interaction domain. The CARD of the cytosolic pathogen receptor Nod1 was overexpressed in Escherichia coli and purified by affinity chromatography and gel filtration. The purified CARD was crystallized at 277 K using the microseeding method. X-ray diffraction data were collected to 1.9 A resolution. The crystals belong to space group P3(1) or P3(2), with unit-cell parameters a = b = 79.1, c = 80.9 A. Preliminary analysis indicates that there is one dimeric CARD molecule in the asymmetric unit.

| S-EPMC2330101 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of human ?-galactosidase.

Project description:?-D-Galactosidase (?-Gal) is an exoglycosidase that cleaves ?-galactosides from glycoproteins, sphingolipids and keratan sulfate. This study reports the expression, purification, crystallization and preliminary X-ray crystallographic analysis of human lysosomal ?-Gal. The sitting-drop vapour-diffusion method was used to crystallize ?-Gal in complexes with its product galactose and with the inhibitor 1-deoxygalactonojirimycin. The resulting crystals were isomorphous and belonged to space group P2(1). The crystals of the ?-Gal-galactose and the ?-Gal-inhibitor complexes had unit-cell parameters a = 94.8, b = 116.1, c = 140.3 Å, ? = 92.2° and a = 94.8, b = 116.0, c = 140.3 Å, ? = 92.2°, respectively. Diffraction data were collected to 1.8 Å resolution for both crystals.

| S-EPMC3253840 | biostudies-literature

Expression, purification, crystallization and preliminary crystallographic analysis of human Pim-1 kinase.

Project description:Pim kinases, including Pim-1, Pim-2 and Pim-3, belong to a distinctive serine/threonine protein-kinase family. They are involved in cytokine-induced signal transduction and the development of lymphoid malignancies. Their kinase domains are highly homologous to one another, but share low sequence identity to other kinases. Specifically, there are two proline residues in the conserved hinge-region sequence ERPXPX separated by a residue that is non-conserved among Pim kinases. Full-length human Pim-1 kinase (1-313) was cloned and expressed in Escherichia coli as a GST-fusion protein and truncated to Pim-1 (14-313) by thrombin digestion during purification. The Pim-1 (14-313) protein was purified to high homogeneity and monodispersity. This protein preparation yielded small crystals in the initial screening and large crystals after optimization. The large crystals of apo Pim-1 enzyme diffracted to 2.1 A resolution and belong to space group P6(5), with unit-cell parameters a = b = 95.9, c = 80.0 A, beta = 120 degrees and one molecule per asymmetric unit.

| S-EPMC1952393 | biostudies-literature

Expression, purification and preliminary crystallographic analysis of human thyroid hormone responsive protein.

Project description:Thyroid hormone responsive protein (Thrsp, also known as Spot 14 and S14) is a carbohydrate-inducible and thyroid-hormone-inducible nuclear protein specific to liver, adipose and lactating mammary tissues. Thrsp functions to activate genes encoding fatty-acid synthesis enzymes. Recent studies have shown that in some cancers human Thrsp (hS14) localizes to the nucleus and is amplified, suggesting that it plays a role in the regulation of lipogenic enzymes during tumourigenesis. Thrsp, a member of the Spot 14 superfamily, is an acidic homodimeric protein with no sequence similarity to other mammalian gene products and its biochemical function is elusive. To shed light on the structure-function relationship of this protein, human Thrsp was crystallized. Recombinant human Thrsp (hThrsp), the N-terminally truncated human Thrsp(10-146) (hThrsp9) and their selenomethionyl (SeMet) derivatives were expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. Diffraction-quality crystals were grown at 293 K using Li(2)SO(4) as a precipitant. Using synchrotron radiation, data for the hThrsp SeMet derivative, hThrsp9 and its SeMet derivative were collected to 4.0, 3.0 and 3.6 Å resolution, respectively, at 100 K. The crystals of full-length hThrsp and its SeMet derivative belonged to space group P4(1)2(1)2, with approximate unit-cell parameters a = b = 123.9, c = 242.1 Å, α = β = γ = 90.0°. In contrast, the crystals of the truncated hThrsp9 and its SeMet derivative belonged to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 91.6, b = 100.8, c = 193.7 Å, α = β = γ = 90.0°. A molecular-replacement solution calculated using a murine Spot 14 structure as a search model indicated the presence of six molecules per asymmetric unit, comprising three hThrsp homodimers.

| S-EPMC3151134 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data