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- PDB-3ls8: Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morphol... -

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Basic information

Entry
Database: PDB / ID: 3ls8
TitleCrystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3
KeywordsTRANSFERASE / ALPHA/BETA PROTEIN / PIK3C3 / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Compound 15e / STRUCTURAL GENOMICS / SGC STOCKHOLM / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / INHIBITOR / PHOSPHATIDYLINOSITOL
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / postsynaptic endosome / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / presynaptic endosome / positive regulation of protein lipidation / positive regulation by host of viral genome replication ...Toll Like Receptor 9 (TLR9) Cascade / postsynaptic endosome / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / presynaptic endosome / positive regulation of protein lipidation / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / protein targeting to lysosome / early endosome to late endosome transport / pexophagy / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / phosphatidylinositol-3-phosphate biosynthetic process / phosphatidylinositol 3-kinase / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autolysosome / synaptic vesicle endocytosis / PI3K Cascade / axoneme / autophagosome assembly / RHO GTPases Activate NADPH Oxidases / autophagosome maturation / regulation of macroautophagy / cellular response to glucose starvation / autophagosome / regulation of cytokinesis / GABA-ergic synapse / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / autophagy / phagocytic vesicle membrane / endocytosis / late endosome / peroxisome / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / protein kinase activity / endosome / regulation of autophagy / cell division / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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 ...Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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. / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AJZ / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Kraulis, P. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Van den Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol
Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Kraulis, P. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Van den Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 3-kinase catalytic subunit type 3
B: Phosphatidylinositol 3-kinase catalytic subunit type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0979
Polymers140,2362
Non-polymers8617
Water4,684260
1
A: Phosphatidylinositol 3-kinase catalytic subunit type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5955
Polymers70,1181
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol 3-kinase catalytic subunit type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5024
Polymers70,1181
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.686, 141.151, 163.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 3-kinase catalytic subunit type 3 / PtdIns-3-kinase type 3 / PI3-kinase type 3 / PI3K type 3 / Phosphoinositide-3-kinase class 3 / ...PtdIns-3-kinase type 3 / PI3-kinase type 3 / PI3K type 3 / Phosphoinositide-3-kinase class 3 / Phosphatidylinositol 3-kinase p100 subunit


Mass: 70118.203 Da / Num. of mol.: 2 / Fragment: UNP Residues 268-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Chemical ChemComp-AJZ / 3-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol


Mass: 313.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O2S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M ammonium acetate, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2009 / Details: mirrors
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.25→70.9 Å / Num. all: 68403 / Num. obs: 68403 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.439 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 12.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.5 / Num. unique all: 9539 / Rsym value: 0.451 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IHY

3ihy


Resolution: 2.25→70.9 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.439 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 3491 5.1 %RANDOM
Rwork0.20862 ---
obs0.21078 64837 99.26 %-
all-64837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.677 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---0.63 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.25→70.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8713 0 54 260 9027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228951
X-RAY DIFFRACTIONr_bond_other_d0.0010.026178
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.98712117
X-RAY DIFFRACTIONr_angle_other_deg0.8533.00115095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88551086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53624.729425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.879151668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0251552
X-RAY DIFFRACTIONr_chiral_restr0.0630.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021716
X-RAY DIFFRACTIONr_mcbond_it0.3761.55378
X-RAY DIFFRACTIONr_mcbond_other0.0761.52142
X-RAY DIFFRACTIONr_mcangle_it0.73728729
X-RAY DIFFRACTIONr_scbond_it1.25133573
X-RAY DIFFRACTIONr_scangle_it2.0464.53377
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 257 -
Rwork0.297 4428 -
obs-4685 93.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6392-2.0588-1.2474.6843-0.40674.9208-0.3533-0.2829-0.52280.12150.12280.10550.2255-0.20870.23060.1693-0.00170.08740.13220.04310.1253-34.478914.23271.8436
21.79470.5781-1.29591.6054-1.15363.4825-0.0217-0.1641-0.10250.1823-0.046-0.11020.04270.14620.06770.03480.0104-0.02450.1013-0.03280.091-10.963625.346-19.9134
31.63690.2587-0.51357.7922-0.86743.09360.00750.15540.1466-0.29570.0923-0.4191-0.16430.1298-0.09980.0267-0.01980.01910.1256-0.04030.0897-12.39938.1405-43.3727
41.9003-0.16430.29780.4404-0.5521.6290.0326-0.05970.1187-0.00060.0380.1015-0.1113-0.1738-0.07060.02860.00320.02530.0489-0.0240.097-38.476535.391-29.9197
512.2094-2.6535-0.25426.92251.51633.9659-0.427-2.2330.04151.94050.6382-0.53690.42760.3317-0.21121.16770.1533-0.17760.8765-0.12240.312-37.050186.67875.9411
62.7185-0.38440.13353.87440.35025.5254-0.0184-0.38630.05830.83210.1289-0.0314-0.1917-0.0373-0.11060.30690.04190.04020.13180.02820.1143-48.487183.2751-15.0353
70.9984-0.8981-0.22512.13810.3990.99670.10320.08550.0665-0.11930.0019-0.1686-0.0118-0.0647-0.10510.1211-0.0190.01610.05970.0550.1675-38.210372.1675-36.3346
82.9599-0.8641-1.09111.57060.51292.9184-0.1181-0.4086-0.05680.56460.4293-0.83080.36780.4588-0.31120.39410.1129-0.30540.2042-0.20040.6042-21.381570.7328-17.6341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A282 - 361
2X-RAY DIFFRACTION2A362 - 562
3X-RAY DIFFRACTION3A563 - 639
4X-RAY DIFFRACTION4A640 - 871
5X-RAY DIFFRACTION5B296 - 353
6X-RAY DIFFRACTION6B354 - 510
7X-RAY DIFFRACTION7B511 - 767
8X-RAY DIFFRACTION8B768 - 871

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