SASDD76: Phox Homologue (PX) - C2 domains of human phosphatidylinositol 4-...

Basic information

• Entry: Database: SASBDB / ID: SASDD76

Sample

Phox Homologue (PX) - C2 domains of human phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (PI3KC2α) in complex with inositol-hexaphosphate (IP6)

• Phox Homology (PX) - C2 domains of human Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (protein), PI3KC2α, Homo sapiens

Function / homology

Function:

vascular associated smooth muscle contraction / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / clathrin coat assembly / membrane organization / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / clathrin-coated vesicle / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / positive regulation of cell migration involved in sprouting angiogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / exocytosis / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / platelet-derived growth factor receptor signaling pathway / positive regulation of autophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatidylinositol binding / trans-Golgi network / epidermal growth factor receptor signaling pathway / endocytosis / insulin receptor signaling pathway / Clathrin-mediated endocytosis / vesicle / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm

Domain/homology:

PI3K-C2-alpha, catalytic domain / Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha, PX domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / C2 domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily

Component:

Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha

• Biological species: Homo sapiens (human)
• Citation: Journal: Structure / Year: 2018; Title: Molecular Basis for Membrane Recruitment by the PX and C2 Domains of Class II Phosphoinositide 3-Kinase-C2α.; Authors: Kai-En Chen / Vikas A Tillu / Mintu Chandra / Brett M Collins / ; Abstract: Phosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated vesicles. A defining feature of the class II PI3Ks is a C-terminal module composed of phox-homology (PX) and C2 membrane interacting domains; however, the mechanisms that control their specific cellular localization remain poorly understood. Here we report the crystal structure of the C2 domain of PI3K-C2α in complex with the phosphoinositide head-group mimic inositol hexaphosphate, revealing two distinct pockets for membrane binding. The C2 domain preferentially binds to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate, and low-resolution structures of the combined PX-C2 module by small-angle X-ray scattering reveal a compact conformation in which cooperative lipid binding by each domain binding can occur. Finally, we demonstrate an unexpected role for calcium in perturbing the membrane interactions of the PX-C2 module, which we speculate may be important for regulating the activity of PI3K-C2α.

Contact author

• Kai-En Chen (The University of Queensland)

Models

• Model #1923: ; Type: dummy / Software: (5.0) / Radius of dummy atoms: 2.25 A / Chi-square value: 0.204; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1958: ; Type: dummy / Radius of dummy atoms: 2.40 A / Chi-square value: 0.204; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1924: ; Type: mix / Software: (5) / Radius of dummy atoms: 2.00 A; Comment: PDB code of PX domain (6BUB) and C2 domain - IP6 complex (6BU0); Chi-square value: 0.17; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Phox Homologue (PX) - C2 domains of human phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (PI3KC2α) in complex with inositol-hexaphosphate (IP6); Specimen concentration: 10.5 mg/ml
• Buffer: Name: 25 mM Tris 200 mM NaCl 5% Glycerol 0.5 mM TCEP 4 mM InsP6; pH: 8.5 ; Comment: 4 mM InsP6 (10 molar excess) was added to the protein sample a day before the data collection

Entity #1041

Name: PI3KC2α / Type: protein
Description: Phox Homology (PX) - C2 domains of human Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
Formula weight: 32.663 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O00443
Sequence:

SNADEPILSF SPKTYSFRQD GRIKEVSVFT YHKKYNPDKH YIYVVRILRE GQIEPSFVFR TFDEFQELHN KLSIIFPLWK LPGFPNRMVL GRTHAKDVAA KRKIELNSYL QSLMNASTDV AECDLVCTFF HPLLRDEKAE GIARSADAGS FSPTPGQIGG AVKLSISYRN GTLFIMVMHI KDLVTEDGAD PNPYVKTYLL PDNHKTSKRK TKISRKTRNP TFNEMLVYSG YSKETLRQRE LQLSVLSAES LRENFFLGGV TLPLKDFNLS KETVKWYQLT AATYL

Experimental information

• Beam: Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Phox Homology (PX) - C2 domains of human phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (PI3KC2α) n complex with inositol-6-phosphate
Measurement date: Oct 20, 2017 / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 15 / Unit: 1/A /

	Min	Max
Q	0.011	0.3509

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 179 /

	Min	Max
Q	0.0124696	0.273391
P(R) point	1	179
R	0	93.43

Result

Type of curve: sec
Comments: SEC-SAXS details: Column type: S200 5/150 GL column; Flow rate: 0.45 ml/min; Sample temperature, 10°C; Sample injection concentration: 10.5 mg/ml. The ab initio models represent the spatially aligned and volume occupancy corrected (averaged) representation of the protein obtained from 20 individual reconstructions (top, DAMFILT model: NSD = 0.66 +/- 0.02; resolution estimate = 3.3 nm) and the best-fit individual DAMMIN reconstruction (bottom) displayed with the corresponding individual model fit to the SAXS data.

	Experimental	Porod
MW	37.27 kDa	28 kDa
Volume	-	47.61 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	0.01979	0.0195	9.9E-5
Radius of gyration, Rg	2.69 nm	2.57 nm	-

	Min	Max
D	-	9.34
Guinier point	6	28