[English] 日本語
Yorodumi- PDB-5x9z: Crystal structure of inositol 1,4,5-trisphosphate receptor large ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x9z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of inositol 1,4,5-trisphosphate receptor large cytosolic domain | ||||||
Components | Inositol 1,4,5-trisphosphate receptor type 1 | ||||||
Keywords | METAL TRANSPORT / receptor channel calcium | ||||||
Function / homology | Function and homology information cGMP effects / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane / epithelial fluid transport ...cGMP effects / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / voluntary musculoskeletal movement / Ion homeostasis / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / GABA-ergic synapse / calcium channel inhibitor activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / sarcoplasmic reticulum / synaptic membrane / liver regeneration / Schaffer collateral - CA1 synapse / cell morphogenesis / positive regulation of insulin secretion / positive regulation of neuron projection development / calcium ion transport / presynapse / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / postsynapse / protein phosphatase binding / transmembrane transporter binding / postsynaptic density / response to hypoxia / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / synapse / dendrite / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.311 Å | ||||||
Authors | Hamada, K. / Miyatake, H. / Terauchi, A. / Mikoshiba, K. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography Authors: Hamada, K. / Miyatake, H. / Terauchi, A. / Mikoshiba, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5x9z.cif.gz | 504.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5x9z.ent.gz | 343.3 KB | Display | PDB format |
PDBx/mmJSON format | 5x9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/5x9z ftp://data.pdbj.org/pub/pdb/validation_reports/x9/5x9z | HTTPS FTP |
---|
-Related structure data
Related structure data | 5gugC 5xa0C 5xa1C 3javS 3uj4S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 252377.312 Da / Num. of mol.: 2 / Fragment: UNP residues 1-2217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itpr1, Insp3r, Pcd6, Pcp1 / Production host: Spodoptera (butterflies/moths) / References: UniProt: P11881 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 7.3→49.1 Å / Num. obs: 10669 / % possible obs: 99.86 % / Redundancy: 11.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 7.311→7.572 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.5745 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 1030 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: fragments of 3JAV C-alpha model and 3UJ4 chain A Resolution: 7.311→49.145 Å / SU ML: 1.71 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 45.04 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 7.311→49.145 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|