Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary crystallographic studies of GRASP65 GRASP domain from Rattus norvegicus.

ABSTRACT: GRASP65 and GRASP55 were classified as Golgi reassembly stacking proteins which play crucial and complementary roles in the stacking of Golgi cisternae. They also participate in vesicle tethering, mitotic progression, the disassembly and reassembly of the Golgi apparatus during mitosis and unconventional secretory pathway regulation. In this study, the expression, crystallization and preliminary crystallographic analysis of the GRASP65 GRASP domain from Rattus norvegicus are presented. The crystals diffracted to 2.0 Å resolution and belonged to space group P21212, with unit-cell parameters a = 44.99, b = 104.29, c = 37.93 Å, ? = ? = ? = 90°. Furthermore, molecular replacement was employed to determine the structure of the GRASP65 GRASP domain from R. norvegicus.

SUBMITTER: Li X

PROVIDER: S-EPMC3702327 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary crystallographic studies of GRASP65 GRASP domain from Rattus norvegicus.

Li Xinxin X Feng Yanbin Y Liu Xinqi X

Acta crystallographica. Section F, Structural biology and crystallization communications 20130628 Pt 7

GRASP65 and GRASP55 were classified as Golgi reassembly stacking proteins which play crucial and complementary roles in the stacking of Golgi cisternae. They also participate in vesicle tethering, mitotic progression, the disassembly and reassembly of the Golgi apparatus during mitosis and unconventional secretory pathway regulation. In this study, the expression, crystallization and preliminary crystallographic analysis of the GRASP65 GRASP domain from Rattus norvegicus are presented. The cryst ...[more]

PMID: 23832210

Similar Datasets

Crystallization and preliminary X-ray crystallographic analysis of the C-terminal domain of guanylate kinase-associated protein from Rattus norvegicus.

Project description:Guanylate kinase-associated protein (GKAP) is a scaffolding protein that plays a role in protein-protein interactions at the synaptic junction such as linking the NMDA receptor-PSD-95 complex to the Shank-Homer complex. In this study, the C-terminal helical domain of GKAP from Rattus norvegicus was purified and crystallized by the vapour-diffusion method. To improve the diffraction quality of the GKAP crystals, a flexible loop in GKAP was truncated and an MBP (maltose-binding protein)-GKAP fusion was constructed in which the last C-terminal helix of MBP is fused to the N-terminus of the GKAP domain. The MBP-GKAP crystals diffracted to 2.0 Å resolution using synchrotron radiation. The crystal was orthorhombic, belonging to space group P2₁2₁2, with unit-cell parameters a=99.1, b=158.7, c=65.5 Å. The Matthews coefficient was determined to be 2.44 Å3 Da(-1) (solvent content 49.5%) with two molecules in the asymmetric unit. Initial attempts to solve the structure by molecular replacement using the MBP structure were successful.

| S-EPMC4089539 | 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, β = 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 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

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, γ = 120.00°.

| S-EPMC3614181 | 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

Crystallization and preliminary crystallographic studies of the complement 1qA globular domain from zebrafish, Dare-C1qAgD.

Project description:Complement 1q (C1q) is the first component of the complement system which can initiate the classical complement pathway. In human, C1q is composed of 18 polypeptide chains: six C1qA chains, six C1qB chains and six C1qC chains. Each chain has a signal peptide and is comprised of a collagen-like region and a C-terminal C1q globular domain (C1qgD), which is organized as a heterotrimer. C1qgD can recognize antigen-antibody complexes containing IgG and IgM or can bind directly to the C-reactive protein. Although the classical complement pathway is found from fish to mammals, only the human C1qgD structure has been determined. Compared with that of mammals, fish C1q exhibits similar immune functions and genome arrangement. In order to illustrate the structure of C1qgD in fish, zebrafish (Danio rerio) C1qA globular domain (Dare-C1qAgD) was expressed, purified and crystallized. X-ray diffraction data were collected from a crystal to a resolution of 2.05 Å; the crystal belonged to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a=50.347, b=85.059, c=95.560 Å. It contained three molecules in the asymmetric unit. The Matthews coefficient value VM was 2.31 Å3 Da(-1), with a calculated solvent content of 46.7%. The data will help to give insight into the structural basis of C1qA in fish species.

| S-EPMC4089530 | biostudies-literature

Crystallization and preliminary crystallographic studies of Helicobacter pylori arginase.

Project description:Helicobacter pylori arginase is an important factor in evasion of the host's immune system and contributes to persistent infection by this bacterium. It is unique in many aspects compared with other arginases: for example, it has optimal activity with Co(2+) as a cofactor rather than Mn(2+) and has strongest activity at acidic pH instead of alkaline pH. In this study, H. pylori arginase was purified and crystallized in complex with Mn(2+) and a diffraction data set was collected to 2.2 Å resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 94.69, b = 102.24, c = 148.61 Å.

| S-EPMC3107149 | biostudies-literature

Crystallization and preliminary crystallographic analysis of human LR11 Vps10p domain.

Project description:Low-density lipoprotein receptor (LDLR) relative with 11 binding repeats (LR11; also known as sorLA) is genetically associated with late-onset Alzheimer's disease and is thought to be involved in neurodegenerative processes. LR11 contains a vacuolar protein-sorting 10 protein (Vps10p) domain. As this domain has been implicated in protein-protein interaction in other receptors, its structure and function are of great biological interest. Human LR11 Vps10p domain was expressed in mammalian cells and the purified protein was crystallized using the hanging-drop vapour-diffusion method. Enzymatic deglycosylation of the sample was critical to obtaining diffraction-quality crystals. Deglycosylated LR11 Vps10p-domain crystals belonged to the hexagonal space group P6(1)22. A diffraction data set was collected to 2.4 Å resolution and a clear molecular-replacement solution was obtained.

| S-EPMC3079991 | 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