Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary crystallographic characterization of three peptidic inhibitors in complex with ?-thrombin.

ABSTRACT: The serine protease thrombin plays a major role in thrombosis and haemostasis. This has driven interest in thrombin inhibitors as potential antithrombotic drugs. Here, the crystallization and preliminary crystallographic analysis of human ?-thrombin in complex with three noncovalent peptide inhibitors of the general sequence D-Phe-Pro-D-Arg-P1'-CONH2 are reported. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1) and diffracted to beyond 1.3?Å resolution.

SUBMITTER: Carvalho Figueiredo A

PROVIDER: S-EPMC3079972 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary crystallographic characterization of three peptidic inhibitors in complex with α-thrombin.

Carvalho Figueiredo Ana A Clement Cristina C CC Philipp Manfred M Barbosa Pereira Pedro José PJ

Acta crystallographica. Section F, Structural biology and crystallization communications 20101221 Pt 1

The serine protease thrombin plays a major role in thrombosis and haemostasis. This has driven interest in thrombin inhibitors as potential antithrombotic drugs. Here, the crystallization and preliminary crystallographic analysis of human α-thrombin in complex with three noncovalent peptide inhibitors of the general sequence D-Phe-Pro-D-Arg-P1'-CONH2 are reported. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1) and diffracted to beyond 1.3 Å resolution. ...[more]

PMID: 21206024

Similar Datasets

Crystallization and preliminary X-ray analysis of the complex of human alpha-thrombin with a modified thrombin-binding aptamer.

Project description:The thrombin-binding aptamer (TBA) is a consensus DNA 15-mer that binds specifically to human alpha-thrombin at nanomolar concentrations and inhibits its procoagulant functions. Recently, a modified TBA (mTBA) containing a 5'-5' inversion-of-polarity site has been shown to be more stable and to possess a higher thrombin affinity than its unmodified counterpart. The structure of the thrombin-TBA complex has previously been determined at low resolution, but did not provide a detailed picture of the aptamer conformation or of the protein-DNA assembly, while that of the complex with mTBA is unknown. Crystallographic analysis of the thrombin-mTBA complex has been attempted. The crystals diffracted to 2.15 A resolution and belonged to space group I222.

| S-EPMC2917304 | biostudies-literature

Crystallization and preliminary crystallographic analysis of human Atg4B-LC3 complex.

Project description:The reversible modification of Atg8 with phosphatidylethanolamine (PE) is crucial for autophagy, the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. Atg4 is a cysteine protease that is responsible for the processing and deconjugation of Atg8. Human Atg4B (HsAtg4B; a mammalian orthologue of yeast Atg4) and LC3 (a mammalian orthologue of yeast Atg8) were expressed and purified and two complexes, one consisting of HsAtg4B(1-354) and LC3(1-120) (complex I; the product complex) and the other consisting of HsAtg4B(1-354) and LC3(1-124) (complex II; the substrate complex), were crystallized using polyethylene glycol 3350 as a precipitant. In both complexes His280 of HsAtg4B was mutated to alanine. The crystals belong to the same space group P2(1)2(1)2(1), with unit-cell parameters a = 47.5, b = 91.8, c = 102.6 A for complex I and a = 46.9, b = 90.9, c = 102.5 A for complex II. Diffraction data were collected to a resolution of 1.9 A from both crystals.

| S-EPMC2330137 | biostudies-literature

Crystallization and preliminary crystallographic analysis of the Tob-hCaf1 complex.

Project description:The Tob/BTG family is a group of antiproliferative proteins that contain two highly homologous regions named Box A and Box B. These proteins all associate with CCR4-associated factor 1 (Caf1), which belongs to the ribonuclease D family of deadenylases. The antiproliferative region of human Tob (residues 1-138) and intact hCaf1 were co-expressed in Escherichia coli, purified and successfully cocrystallized. The crystal belongs to the tetragonal space group I422, with unit-cell parameters a = b = 150.9, c = 113.9 A, and is estimated to contain one heterodimer per asymmetric unit. The crystal diffracted to around 2.6 A resolution.

| S-EPMC2344109 | biostudies-literature

Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus-Ufc1 complex.

Project description:Human Uba5, which contains an adenylation domain and a C-terminal region, is the smallest ubiquitin-like molecule-activating enzyme. The mechanism through which the enzyme recognizes Ufc1 and catalyzes the formation of the Ufc1-Ufm1 complex remains unknown. In this study, Uba5 residues 364-404 were demonstrated to be necessary for the transthiolation of Ufm1 to Ufc1, and Uba5 381-404 was identified to be the minimal region for Ufc1 recognition. The fusion protein between Uba5 381-404 and Ufc1 was cloned, expressed and purified, and exists as a homodimer in solution. Crystallization was performed at 293?K using PEG 4000 as precipitant; the optimized crystals diffracted to 3.0?Å resolution and had unit-cell parameters a = b = 82.49, c = 62.47?Å, ? = ? = 90, ? = 120°. With one fusion-protein molecule in the asymmetric unit, the Matthews coefficient and solvent content were calculated to be 2.55?Å(3)?Da(-1) and 51.84%, respectively.

| S-EPMC4118812 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of the marine α-amylase AmyP.

Project description:AmyP is a raw-starch-degrading α-amylase newly identified from a marine metagenome library. It shares low sequence similarity with characterized glycoside hydrolases and was classified into a new subfamily of GH13. In particular, it showed preferential degradation to raw rice starch. Full-length AmyP was cloned and overexpressed in Escherichia coli, then purified and crystallized in the presence of its substrate analogue β-cyclodextrin. X-ray diffraction data were collected to a resolution of 2.1 Å. The crystal belonged to space group P2₁2₁2, with unit-cell parameters a=129.824, b=215.534, c=79.699 Å, α=β=γ=90°, and was estimated to contain two molecules in one asymmetric unit.

| S-EPMC3606570 | biostudies-literature

Crystallization and preliminary crystallographic characterization of glutamine synthetase from Medicago truncatula.

Project description:The condensation of ammonium and glutamate into glutamine catalyzed by glutamine synthetase (GS) is a fundamental step in nitrogen metabolism in all kingdoms of life. In plants, this is preceded by the reduction of inorganic nitrogen to an ammonium ion and therefore effectively articulates nitrogen fixation and metabolism. Although the three-dimensional structure of the dodecameric bacterial GS was determined quite some time ago, the quaternary architecture of the plant enzyme has long been assumed to be octameric, mostly on the basis of low-resolution electron-microscopy studies. Recently, the crystallographic structure of a monocotyledonous plant GS was reported that revealed a homodecameric organization. In order to unambiguously establish the quaternary architecture of GS from dicotyledonous plants, GS1a from the model legume Medicago truncatula was overexpressed, purified and crystallized. The collection of synchrotron diffraction data to 2.35 A resolution allowed the determination of the three-dimensional structure of this enzyme by molecular replacement.

| S-EPMC2802889 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of importin-α from Neurospora crassa.

Project description:Importin-α recognizes cargo proteins that contain classical nuclear localization sequences (NLS) and, in complex with importin-β, is able to translocate nuclear proteins through the nuclear pore complex. The filamentous fungus Neurospora crassa is a well studied organism that has been widely used as a model organism for fundamental aspects of eukaryotic biology, and is important for understanding the specific mechanisms of protein transport to the cell nucleus. In this work, the crystallization and preliminary X-ray diffraction analysis of importin-α from N. crassa (IMPα-Nc) complexed with a classical NLS peptide (SV40 NLS) are reported. IMPα-Nc-SV40 NLS crystals diffracted X-rays to 2.0 Å resolution and the structure was solved by molecular-replacement techniques, leading to a monomeric structure. The observation of the electron-density map indicated the presence of SV40 NLSs interacting at both the minor and major NLS-binding sites of the protein.

| S-EPMC3976073 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase-RNA complex.

Project description:The sulfurtransferase 4-thiouridine synthetase (ThiI) is involved in the ATP-dependent modification of U8 in tRNA. ThiI from Thermotoga maritima was cloned, overexpressed and purified. A complex comprising ThiI and a truncated tRNA was prepared and crystallized, and X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 102.9, b = 112.8, c = 132.8 Å.

| S-EPMC3614169 | biostudies-literature

Crystallization and preliminary X-ray crystallographic characterization of a public CMV-specific TCR in complex with its cognate antigen.

Project description:The T-cell response to human cytomegalovirus is characterized by a dramatic reduction of clonal diversity in patients undergoing chronic inflammation or immunodepression. In order to check whether all the selected high-avidity T-cell clones recognize the immunodominant pp65 peptide antigen pp65(495-503) (NLVPMVATV) presented by the major histocompatibility complex (MHC) molecule HLA-A2 in a similar manner, several public high-affinity T-cell receptors (TCRs) specific for the pp65(495-503)-HLA-A2 complex have been investigated. Expression, purification and crystallization were performed and preliminary crystallographic data were collected to 4.7 angstrom resolution for the RA15 TCR in complex with the pp65(495-503)-HLA-A2 complex. Comparison of the RA15-pp65(495-503)-HLA-A2 complex molecular-replacement solution with the structure of another high-affinity pp65(495-503)-HLA-A2-specific TCR, RA14, shows a shared docking mode, indicating that the clonal focusing could be accompanied by the selection of a most favoured peptide-readout mode. However, the position of the RA15 V beta domain is significantly shifted, suggesting a different interatomic interaction network.

| S-EPMC2777048 | biostudies-literature

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the chicken CD8??-BF2*0401 complex.

Project description:In the process of antigen presentation, the MHCI-CD8 complex is important for immune signal transduction by the activation of cytotoxic T cells. Here, the expression, purification, crystallization and X-ray analysis of the complex of the chicken MHC class I molecule BF2*0401 and CD8?? (CD8??-BF2*0401) are reported. This complex was verified by SDS-PAGE analysis of a CD8??-BF2*0401 crystal, which showed three bands corresponding to the molecular weights of BF2*0401, ?2-microglobulin and CD8?, respectively. The crystal of CD8??-BF2*0401 diffracted to 2.8?Å resolution and belonged to space group P21, with unit-cell parameters a = 90.6, b = 90.8, c = 94.9?Å, ? = 98°. The Matthews coefficient and solvent content were calculated to be 2.88?Å(3)?Da(-1) and ?57.3%, respectively.

| S-EPMC4157433 | 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