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- PDB-3i5r: PI3K SH3 domain in complex with a peptide ligand -

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Basic information

Entry
Database: PDB / ID: 3i5r
TitlePI3K SH3 domain in complex with a peptide ligand
Components
  • Peptide ligand
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
KeywordsPROTEIN BINDING / SH3 domain / peptide complex / Alternative splicing / Disease mutation / Host-virus interaction / Phosphoprotein / Polymorphism / SH2 domain / Ubl conjugation
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / phosphatidylinositol 3-kinase complex / T follicular helper cell differentiation / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / kinase activator activity / Nephrin family interactions / Signaling by LTK in cancer / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / negative regulation of stress fiber assembly / RND1 GTPase cycle / positive regulation of filopodium assembly / RND2 GTPase cycle / RND3 GTPase cycle / insulin binding / growth hormone receptor signaling pathway / Signaling by ALK / RHOV GTPase cycle / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / negative regulation of osteoclast differentiation / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / PI3K events in ERBB2 signaling / insulin receptor substrate binding / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOG GTPase cycle / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / Interleukin receptor SHC signaling / GAB1 signalosome / Role of phospholipids in phagocytosis / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by FGFR4 in disease / positive regulation of lamellipodium assembly / Signaling by FLT3 ITD and TKD mutants / GPVI-mediated activation cascade / Signaling by FGFR3 in disease / Tie2 Signaling / insulin-like growth factor receptor binding / Signaling by FGFR2 in disease / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / phosphotyrosine residue binding / Signaling by FGFR1 in disease / Interleukin-7 signaling / Downstream signal transduction / substrate adhesion-dependent cell spreading / B cell differentiation / osteoclast differentiation / insulin-like growth factor receptor signaling pathway / response to endoplasmic reticulum stress / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases ...Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH3 Domains / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBatra-Safferling, R. / Granzin, J. / Modder, S. / Hoffmann, S. / Willbold, D.
CitationJournal: Biol.Chem. / Year: 2010
Title: Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding.
Authors: Batra-Safferling, R. / Granzin, J. / Modder, S. / Hoffmann, S. / Willbold, D.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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
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 3-kinase regulatory subunit alpha
B: Peptide ligand


Theoretical massNumber of molelcules
Total (without water)10,7812
Polymers10,7812
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-3 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.365, 60.365, 46.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

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Components

#1: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PI3-kinase p85 subunit alpha / PtdIns-3-kinase p85-alpha / PI3K


Mass: 9436.354 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 1-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB1, PIK3R1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P27986
#2: Protein/peptide Peptide ligand


Mass: 1344.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: artificial peptide ligand
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10.5
Details: 100mM CAPS, 2M ammonium sulfate, 0.2M lithium sulfate, pH 10.5, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→22.79 Å / Num. all: 11100 / Num. obs: 11076 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 18.12 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 26.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1pht

1pht


Resolution: 1.7→22.789 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.19 / σ(F): 0.07 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 520 4.75 %
Rwork0.1817 10422 -
obs0.1836 10942 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.527 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso max: 71.14 Å2 / Biso mean: 22.183 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.438 Å2-0 Å2-0 Å2
2--0.438 Å20 Å2
3----0.877 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 0 67 781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008730
X-RAY DIFFRACTIONf_angle_d1.254987
X-RAY DIFFRACTIONf_dihedral_angle_d19.358268
X-RAY DIFFRACTIONf_chiral_restr0.092100
X-RAY DIFFRACTIONf_plane_restr0.006132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.87120.22831210.17882508X-RAY DIFFRACTION96
1.8712-2.14180.19951470.15472560X-RAY DIFFRACTION99
2.1418-2.69780.20381350.1712604X-RAY DIFFRACTION99
2.6978-22.79060.23791170.19222750X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.4458-0.2215-0.07950.92080.22131.0102-0.0561-0.0626-0.10740.11510.0120.13430.08930.00960.03090.10020.00690.01010.10280.01880.11623.270825.194419.1911
26.1208-0.8906-0.94222.84570.90280.2893-0.2419-0.38170.0330.76940.10790.18050.13580.05010.13290.1805-0.00340.00990.20450.01550.1489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 82
2X-RAY DIFFRACTION2chain BB3 - 11

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