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- PDB-2b3r: Crystal structure of the C2 domain of class II phosphatidylinosit... -

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Basic information

Entry
Database: PDB / ID: 2b3r
TitleCrystal structure of the C2 domain of class II phosphatidylinositide 3-kinase C2
ComponentsPhosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
KeywordsTRANSFERASE / C2 domain / lipid binding / PI3-kinase
Function / homology
Function and homology information


negative regulation of zinc ion transmembrane transport / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the plasma membrane / autophagosome organization / Golgi Associated Vesicle Biogenesis / phosphatidylinositol-4-phosphate 3-kinase / Clathrin-mediated endocytosis / phosphatidylinositol 3-kinase complex ...negative regulation of zinc ion transmembrane transport / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the plasma membrane / autophagosome organization / Golgi Associated Vesicle Biogenesis / phosphatidylinositol-4-phosphate 3-kinase / Clathrin-mediated endocytosis / 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 / phosphatidylinositol 3-kinase / clathrin-coated vesicle / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / clathrin binding / positive regulation of cell migration involved in sprouting angiogenesis / exocytosis / positive regulation of autophagy / cellular response to starvation / phosphatidylinositol binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / macroautophagy / trans-Golgi network / endocytosis / vesicle / phosphorylation / intracellular membrane-bounded organelle / nucleoplasm / ATP binding / 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
Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, L. / Song, X. / He, D. / Komma, C. / Kita, A. / Verbasius, J.V. / Bellamy, H. / Miki, K. / Czech, M.P. / Zhou, G.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the C2 domain of class II phosphatidylinositide 3-kinase C2alpha.
Authors: Liu, L. / Song, X. / He, D. / Komma, C. / Kita, A. / Virbasius, J.V. / Huang, G. / Bellamy, H.D. / Miki, K. / Czech, M.P. / Zhou, G.W.
History
DepositionSep 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 alpha polypeptide
B: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5008
Polymers30,9232
Non-polymers5766
Water4,107228
1
A: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7504
Polymers15,4621
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7504
Polymers15,4621
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
B: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
hetero molecules

A: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
B: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,00016
Polymers61,8474
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7210 Å2
ΔGint-226 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.365, 53.365, 200.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21B-301-

SO4

DetailsTwo molecules are related by an NCS symmetry. Two kinds of dimerization interfaces may be existing.

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Components

#1: Protein Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide / Phosphoinositide 3-Kinase-C2-alpha / PtdIns-3-kinase C2 alpha / PI3K-C2alpha / Cpk-m / p170


Mass: 15461.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pik3c2a, Cpk / Production host: Escherichia coli (E. coli)
References: UniProt: Q61194, phosphatidylinositol-4-phosphate 3-kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6K, Li2SO4, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONCAMD GCPCC21.384
Detector
TypeIDDetector
MARRESEARCH1CCD
MARRESEARCH2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.3841
ReflectionResolution: 2.3→50 Å / Num. all: 13733 / Num. obs: 13692 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 695 randomly selected 5% of observed reflections
Rwork0.197 --
all0.198 13677 -
obs0.197 13622 -
Refinement stepCycle: LAST / Resolution: 2.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 30 228 2252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d26.6

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