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- PDB-3ihy: Human PIK3C3 crystal structure -

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Basic information

Entry
Database: PDB / ID: 3ihy
TitleHuman PIK3C3 crystal structure
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3
KeywordsTRANSFERASE / Alpha/Beta protein / Structural Genomics / SGC Stockholm / Structural Genomics Consortium / SGC / ATP-binding / Kinase / Manganese / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity ...Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / 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 / phagophore assembly site / phosphatidylinositol-mediated signaling / Translation of Replicase and Assembly of the Replication Transcription Complex / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / axoneme / autophagosome maturation / phosphatidylinositol phosphate biosynthetic process / autophagosome assembly / RHO GTPases Activate NADPH Oxidases / PI3K Cascade / regulation of macroautophagy / cellular response to glucose starvation / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / autophagy / peroxisome / endocytosis / phagocytic vesicle membrane / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / kinase activity / midbody / endosome / protein kinase activity / cell cycle / cell division / phosphorylation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / 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. ...Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / 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. / 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
Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSiponen, M.I. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Siponen, M.I. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Kotzsch, A. / Kragh Nielsen, T. / Moche, M. / Nyman, T. / Persson, C. / Roos, A.K. / Sagemark, J. / Schueler, H. / Schutz, P. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Human PIK3C3 crystal structure
Authors: Siponen, M.I. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Siponen, M.I. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Kotzsch, A. / Kragh Nielsen, T. / Moche, M. / Nyman, T. / Persson, C. / Roos, A.K. / Sagemark, J. / Schueler, H. / Schutz, P. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Phosphatidylinositol 3-kinase catalytic subunit type 3
D: Phosphatidylinositol 3-kinase catalytic subunit type 3
E: Phosphatidylinositol 3-kinase catalytic subunit type 3


Theoretical massNumber of molelcules
Total (without water)342,7825
Polymers342,7825
Non-polymers00
Water181
1
A: Phosphatidylinositol 3-kinase catalytic subunit type 3


Theoretical massNumber of molelcules
Total (without water)68,5561
Polymers68,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol 3-kinase catalytic subunit type 3


Theoretical massNumber of molelcules
Total (without water)68,5561
Polymers68,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphatidylinositol 3-kinase catalytic subunit type 3


Theoretical massNumber of molelcules
Total (without water)68,5561
Polymers68,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphatidylinositol 3-kinase catalytic subunit type 3


Theoretical massNumber of molelcules
Total (without water)68,5561
Polymers68,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phosphatidylinositol 3-kinase catalytic subunit type 3


Theoretical massNumber of molelcules
Total (without water)68,5561
Polymers68,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.297, 96.491, 150.679
Angle α, β, γ (deg.)107.77, 91.75, 92.41
Int Tables number1
Space group name H-MP1

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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: 68556.336 Da / Num. of mol.: 5 / Fragment: UNP residues 282-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, PIK3C3A / Plasmid: pNIC Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium acetate 25% PEG3350 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2009 / Details: mirrors
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→19.84 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.84 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.662 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25505 4076 5 %RANDOM
Rwork0.18663 ---
obs0.19006 77091 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.483 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20.01 Å2
2---0.01 Å2-0.01 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.285 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21669 0 0 1 21670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222121
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215313
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.98229894
X-RAY DIFFRACTIONr_angle_other_deg0.96337483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26552665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.524.7541056
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63154153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.47815130
X-RAY DIFFRACTIONr_chiral_restr0.0780.23344
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0224136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024254
X-RAY DIFFRACTIONr_nbd_refined0.2360.25444
X-RAY DIFFRACTIONr_nbd_other0.2040.215933
X-RAY DIFFRACTIONr_nbtor_refined0.190.210898
X-RAY DIFFRACTIONr_nbtor_other0.0940.211901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2445
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0640.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.2128
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1081.517162
X-RAY DIFFRACTIONr_mcbond_other0.0831.55336
X-RAY DIFFRACTIONr_mcangle_it1.018221670
X-RAY DIFFRACTIONr_scbond_it1.818310048
X-RAY DIFFRACTIONr_scangle_it2.614.58224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 275 -
Rwork0.282 5633 -
obs--98.47 %

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