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- PDB-6btz: Crystal structure of the PI3KC2alpha C2 domain in space group C121 -

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Basic information

Entry
Database: PDB / ID: 6btz
TitleCrystal structure of the PI3KC2alpha C2 domain in space group C121
ComponentsPhosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
KeywordsTRANSFERASE / C2 domain / lipid binding / phosphoinositide / PI3-kinase
Function / homology
Function and homology information


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 ...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 / clathrin binding / positive regulation of cell migration involved in sprouting angiogenesis / Golgi Associated Vesicle Biogenesis / exocytosis / Synthesis of PIPs at the plasma membrane / platelet-derived growth factor receptor signaling pathway / positive regulation of autophagy / phosphatidylinositol binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / trans-Golgi network / epidermal growth factor receptor signaling pathway / endocytosis / insulin receptor signaling pathway / Clathrin-mediated endocytosis / vesicle / phosphorylation / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / C2 domain / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain ...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 / C2 domain / 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. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsChen, K.-E. / Collins, B.M.
CitationJournal: Structure / Year: 2018
Title: Molecular Basis for Membrane Recruitment by the PX and C2 Domains of Class II Phosphoinositide 3-Kinase-C2 alpha.
Authors: Chen, K.E. / Tillu, V.A. / Chandra, M. / Collins, B.M.
History
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
B: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
C: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
D: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,54433
Polymers59,7774
Non-polymers3,76829
Water7,296405
1
A: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,13310
Polymers14,9441
Non-polymers1,1899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,96510
Polymers14,9441
Non-polymers1,0219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7818
Polymers14,9441
Non-polymers8377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6655
Polymers14,9441
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.346, 61.546, 90.496
Angle α, β, γ (deg.)90.000, 92.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1816-

HOH

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Components

#1: Protein
Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha / PtdIns-3-kinase C2 subunit alpha / Phosphoinositide 3-kinase-C2-alpha


Mass: 14944.179 Da / Num. of mol.: 4 / Fragment: C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C2A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O00443, phosphatidylinositol-4-phosphate 3-kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 % / Mosaicity: 0.21 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→46.4 Å / Num. obs: 49805 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 17.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.045 / Rrim(I) all: 0.123 / Net I/σ(I): 10.3 / Num. measured all: 368396
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.8870.682063529540.840.2730.7342.496.3
9.04-46.46.80.04630824510.9980.0190.0524.698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.4 Å
Translation2.5 Å46.4 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.25data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3R

2b3r


Resolution: 1.85→46.395 Å / FOM work R set: 0.8586 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2148 2525 5.07 %
Rwork0.1866 47267 -
obs0.1881 49792 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.99 Å2 / Biso mean: 21.61 Å2 / Biso min: 7.71 Å2
Refinement stepCycle: final / Resolution: 1.85→46.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 224 405 4663
Biso mean--42.29 29 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074367
X-RAY DIFFRACTIONf_angle_d1.1395858
X-RAY DIFFRACTIONf_chiral_restr0.048643
X-RAY DIFFRACTIONf_plane_restr0.004699
X-RAY DIFFRACTIONf_dihedral_angle_d13.8991726
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.88080.27841340.24872502263696
1.8808-1.91920.27351230.209626332756100
1.9192-1.96090.24591560.198826062762100
1.9609-2.00650.24481500.187725662716100
2.0065-2.05670.22681410.189226682809100
2.0567-2.11230.23241440.184625962740100
2.1123-2.17450.22581460.187426032749100
2.1745-2.24470.22191390.180826102749100
2.2447-2.32490.25921650.189426102775100
2.3249-2.4180.23061330.18926452778100
2.418-2.5280.23821350.185826162751100
2.528-2.66130.25281600.200126362796100
2.6613-2.8280.23251220.197826232745100
2.828-3.04630.25551220.198326712793100
3.0463-3.35280.20161390.192126502789100
3.3528-3.83770.18761330.172126662799100
3.8377-4.83430.15271520.150226332785100
4.8343-46.41010.20561310.199627332864100

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