[English] 日本語
![](img/lk-miru.gif)
- PDB-2v1y: Structure of a phosphoinositide 3-kinase alpha adaptor-binding do... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2v1y | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a phosphoinositide 3-kinase alpha adaptor-binding domain (ABD) in a complex with the iSH2 domain from p85 alpha | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / KINASE / CANCER / SH2 DOMAIN / SH3 DOMAIN / ONCOGENIC MUTATIONS / HOST-VIRUS INTERACTION / PHOSPHORYLATION / DISEASE MUTATION / PHOSPHOINOSITIDE / PHOSPHOLIPID / PHOSPHOLIPID SIGNALLING / PHOSPHOINOSITIDE 3-KINASE / SIGNAL TRANSDUCTION | ||||||
Function / homology | ![]() : / : / : / : / PI3K events in ERBB4 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade ...: / : / : / : / PI3K events in ERBB4 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / Interleukin receptor SHC signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI3K Cascade / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / DAP12 signaling / Regulation of signaling by CBL / perinuclear endoplasmic reticulum membrane / RET signaling / regulation of toll-like receptor 4 signaling pathway / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / positive regulation of gene expression via chromosomal CpG island demethylation / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / RHOF GTPase cycle / kinase activator activity / phosphatidylinositol 3-kinase complex, class IB / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / Extra-nuclear estrogen signaling / positive regulation of leukocyte migration / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / G alpha (q) signalling events / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / protein kinase activator activity / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miled, N. / Yan, Y. / Hon, W.C. / Perisic, O. / Zvelebil, M. / Inbar, Y. / Schneidman-Duhovny, D. / Wolfson, H.J. / Backer, J.M. / Williams, R.L. | ||||||
![]() | ![]() Title: Mechanism of Two Classes of Cancer Mutations in the Phosphoinositide 3-Kinase Catalytic Subunit. Authors: Miled, N. / Yan, Y. / Hon, W.C. / Perisic, O. / Zvelebil, M. / Inbar, Y. / Schneidman-Duhovny, D. / Wolfson, H.J. / Backer, J.M. / Williams, R.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12821.479 Da / Num. of mol.: 1 / Fragment: ADAPTOR-BINDING DOMAIN, RESIDUES 1-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: CHAIN A IS THE ADAPTOR-BINDING DOMAIN FROM BOVINE P110 ALPHA Plasmid: POPCG / Production host: ![]() ![]() References: UniProt: P32871, phosphatidylinositol-4,5-bisphosphate 3-kinase |
---|---|
#2: Protein | Mass: 21223.402 Da / Num. of mol.: 1 / Fragment: INTER-SH2 DOMAIN (ISH2), RESIDUES 431-600 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: CHAIN B IS THE ISH2 DOMAIN FROM HUMAN P85 ALPHA Plasmid: POPCG / Production host: ![]() ![]() References: UniProt: P27986, phosphatidylinositol-4,5-bisphosphate 3-kinase |
#3: Water | ChemComp-HOH / |
Compound details | PHOSPHORYLATES PTDINS, PTDINS4P AND PTDINS(4,5)P2. BINDS TO ACTIVATED (PHOSPHORYLATED) PROTEIN-TYR ...PHOSPHORYL |
Sequence details | ADAPTOR-BINDING DOMAIN, RESIDUES 1-108 RESIDUES 431-600 OF HUMAN P85 ALPHA |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | pH: 7 Details: 0.2M MG(NO3)2, 20% PEG3350 (HAMPTON), 5MM TRIS-HCL PH 7.0 (25C), 5% GLYCEROL AND 5MM FRESH DTT |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Details: BENT MIRROR | |||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.4→47.67 Å / Num. obs: 10926 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.53 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.48 | |||||||||
Reflection shell | Resolution: 2.4→2.42 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.32 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.99 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|