Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Preliminary X-ray crystallographic studies of the TRAF domain of human TRAF4.

ABSTRACT: TNF receptor-associated factor (TRAF) proteins were initially identified as tumour necrosis factor receptor (TNFR)-interacting proteins that perform critical functions in the regulation of inflammation, antiviral responses and apoptosis. Although TRAF4 is a canonical TRAF protein, it contains a unique domain boundary and functions differently in the cell. In this study, the human TRAF4 TRAF domain, corresponding to amino acids 290-470, was overexpressed in Escherichia coli using engineered C-terminal His tags. The TRAF4 TRAF domain was then purified to homogeneity and crystallized at 293?K. Finally, X-ray diffraction data were collected to a resolution of 2.3?Å from a crystal belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.9, b = 87.9, c = 117.3?Å, ? = ? = ? = 90°.

SUBMITTER: Yoon JH

PROVIDER: S-EPMC3758155 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Preliminary X-ray crystallographic studies of the TRAF domain of human TRAF4.

Yoon Jong Hwan JH Park Hyun Ho HH

Acta crystallographica. Section F, Structural biology and crystallization communications 20130821 Pt 9

TNF receptor-associated factor (TRAF) proteins were initially identified as tumour necrosis factor receptor (TNFR)-interacting proteins that perform critical functions in the regulation of inflammation, antiviral responses and apoptosis. Although TRAF4 is a canonical TRAF protein, it contains a unique domain boundary and functions differently in the cell. In this study, the human TRAF4 TRAF domain, corresponding to amino acids 290-470, was overexpressed in Escherichia coli using engineered C-ter ...[more]

PMID: 23989155

Similar Datasets

Preliminary X-ray crystallographic studies of the short form of the human TRAF4 TRAF domain.

Project description:TNF (tumour necrosis factor) receptor-associated factor 4 (TRAF4) is a unique TRAF protein that participates in morphogenetic and developmental function and cell migration. TRAF-family proteins contain a TRAF domain for target interaction. In this study, the short form of the human TRAF4 TRAF domain, corresponding to amino acids 290-462, was overexpressed in Escherichia coli using engineered C-terminal His tags. The short form of the TRAF4 TRAF domain was purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 4.2 Å from a crystal belonging to the hexagonal space group P3?, with unit-cell parameters a = b = 147.17, c = 202.69 Å.

| S-EPMC3729174 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of the PYD domain of human NALP3.

Project description:The NALP3 inflammasome is a macromolecular complex that is responsible for the innate immune response against infection by bacterial and viral pathogens. The NALP3 inflammasome is composed of three protein components: NALP3, ASC and caspase 1. Interaction between NALP3 and ASC via PYD domains is critical for the assembly of the NALP3 inflammasome. In this study, human NALP3 PYD, corresponding to amino acids 3-110, was overexpressed in Escherichia coli using engineered C-terminal His tags. NALP3 PYD was then purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 1.7 Å from a crystal belonging to the primitive monoclinic space group P2(1), with unit-cell parameters a = 42.03, b = 60.14, c = 51.61 Å, ? = 107.40°.

| S-EPMC3212466 | biostudies-literature

Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6.

Project description:Toll-like receptor (TLR) proteins have been identified and shown to play a role in the innate immune response. TLR6 associated with TLR2 can recognize diacylated lipoprotein. In this study, the human TLR6 TIR domain corresponding to amino acids 640-796 was overexpressed in Escherichia coli using engineered C-terminal His tags. The TLR6 TIR domain was then purified to homogeneity and crystallized at 20°C. Finally, X-ray diffraction data were collected to a resolution of 2.2?Å from a crystal belonging to space group C2, with unit-cell parameters a = 127.60, b = 44.20, c = 75.72?Å, ? = 118.89°

| S-EPMC4118802 | biostudies-literature

Filament-like DREP4 CIDE domain: characterization and preliminary X-ray crystallographic studies.

Project description:DREP4 is a nuclease from fruit fly that is involved in apoptotic DNA fragmentation. DREP4 contains a conserved CIDE domain that acts as a protein-interaction module and is critical for its function. In this study, it was found that DREP4 CIDE domains form filament-like structures in solution. The length of the highly ordered filament-like structure is dependent on the salt concentration. By adjusting the salt concentration the DREP4 CIDE domain could be crystallized, and X-ray diffraction data were collected to a resolution of 1.9?Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 53.08, b = 76.58, c = 174.59?Å.

| S-EPMC5544006 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain.

Project description:Drep2 is a novel nuclease from the fruit fly that might have a similar function in apoptosis to DFF40 and DFF45, which are primary players in apoptotic DNA fragmentation. Drep2 contains a conserved CIDE domain of ?90 amino-acid residues that is involved in protein-protein interaction. In this study, the Drep2 CIDE domain was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to a resolution of 2.3?Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37?Å.

| S-EPMC4188092 | biostudies-literature

Expression, crystallization and preliminary X-ray crystallographic studies of SCP3 coiled-coil domain.

Project description:The synaptonemal complex protein SCP3 is one of the components of the lateral element of the synaptonemal complex, which is a meiosis-specific complex structure formed at the synapse of homologous chromosomes. In this study, a C-terminal coiled-coil domain, SCP3, was overexpressed in Escherichia coli with an engineered C-terminal His tag. The coiled-coil domain of SCP3 was then purified to homogeneity and crystallized at 293?K. X-ray diffraction data were collected to a resolution of 3.2?Å from a crystal belonging to space group C2, with unit-cell parameters a = 121.29, b = 43.08, c = 57.42?Å, ? = 100.71°. The asymmetric unit was estimated to contain three molecules.

| S-EPMC3818053 | biostudies-literature

Purification, crystallization and preliminary x-ray crystallographic studies of RAIDD Death-Domain (DD).

Project description:Caspase-2 activation by formation of PIDDosome is critical for genotoxic stress induced apoptosis. PIDDosome is composed of three proteins, RAIDD, PIDD, and Caspase-2. RAIDD is an adaptor protein containing an N-terminal Caspase-Recruiting-Domain (CARD) and a C-terminal Death-Domain (DD). Its interactions with Caspase-2 and PIDD through CARD and DD respectively and formation of PIDDosome are important for the activation of Caspase-2. RAIDD DD cloned into pET26b vector was expressed in E. coli cells and purified by nickel affinity chromatography and gel filtration. Although it has been known that the most DDs are not soluble in physiological condition, RAIDD DD was soluble and interacts tightly with PIDD DD in physiological condition. The purified RAIDD DD alone has been crystallized. Crystals are trigonal and belong to space group P3(1)21 (or its enantiomorph P3(2)21) with unit-cell parameters a = 56.3, b = 56.3, c = 64.9 A and gamma = 120 degrees . The crystals were obtained at room temperature and diffracted to 2.0 A resolution.

| S-EPMC2705503 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of the coiled-coil domain of PIST.

Project description:PIST [PDZ (PSD-95, Discs-large and ZO-1) protein interacting specifically with TC10] functions as a regulator of membrane trafficking with Rab6A. Recently, the involvement of the fusion of PIST with ROS1 in cancer development has been identified. In this study, the coiled-coil domain of PIST, which is the domain responsible for interaction with Rab6A and fusion with ROS1, corresponding to amino acids 29-133, was overexpressed in Escherichia coli using engineered C-terminal His tags. The coiled-coil domain of PIST was then purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 4.0 Å from a crystal belonging to the hexagonal space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 85.19, c = 240.09 Å, ? = 120.00°.

| S-EPMC3614181 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of human ribosomal protein L7a (RPL7a).

Project description:Ribosomal proteins are a major component of ribosomes, which catalyze protein synthesis. One ribosomal protein, L7a (RPL7a), which is a component of the 60S large ribosomal subunit, has additional functions involved in cell growth and differentiation that occur via interaction with human thyroid hormone receptor (THR) and retinoic acid receptor (RAR) and in turn inhibit the activities of the two nuclear hormone receptors. In this study, the N-terminal domain of human RPL7a was overexpressed in Escherichia coli using an engineered C-terminal His tag. The N-terminal domain of human RPL7a was then purified to homogeneity and crystallized at 293?K. X-ray diffraction data were collected to a resolution of 3.5?Å from a crystal belonging to the tetragonal space group P4(1)22 or P4(3)22 with unit-cell parameters a = 92.28, b = 92.28, c = 236.59?Å.

| S-EPMC3080163 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of the CIDE-N domain of CIDE-3.

Project description:The CIDE-3 protein plays a critical role in lipid metabolism by its involvement in lipid droplet formation. CIDE-3 contains two conserved cell-death-inducing DFF45-like effector (CIDE) domains (CIDE-N at the N-terminus and CIDE-C at the C-terminus) of ∼90 amino-acid residues that are involved in protein-protein interaction. In this study, the CIDE-N domain of CIDE-3 was purified and crystallized by the hanging-drop vapour-diffusion method and X-ray diffraction data were collected from the crystals to a resolution of 2.0 Å. The crystals were found to belong to space group P3(2), with unit-cell parameters a = b = 63.35, c = 37.60 Å, γ = 120°.

| S-EPMC3818048 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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