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- PDB-2iui: Crystal structure of the PI3-kinase p85 N-terminal SH2 domain in ... -

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Basic information

Entry
Database: PDB / ID: 2iui
TitleCrystal structure of the PI3-kinase p85 N-terminal SH2 domain in complex with PDGFR phosphotyrosyl peptide
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Platelet-derived growth factor receptor beta
KeywordsTRANSFERASE / PHOSPHORYLATION / P85 / SH2 / PI3K / SH2 DOMAIN / SH3 DOMAIN / PI3-KINASE / DISEASE MUTATION
Function / homology
Function and homology information


platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis ...platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / perinuclear endoplasmic reticulum membrane / cardiac myofibril assembly / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol metabolic process / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / positive regulation of chemotaxis / PI3K events in ERBB4 signaling / Signaling by PDGF / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / 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 / RHOF GTPase cycle / kinase activator activity / transmembrane receptor protein tyrosine kinase adaptor activity / platelet-derived growth factor receptor binding / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of leukocyte migration / positive regulation of filopodium assembly / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / insulin binding / positive regulation of DNA biosynthetic process / RHOV GTPase cycle / RHOB GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / positive regulation of smooth muscle cell migration / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / positive regulation of calcium ion import / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / platelet-derived growth factor receptor-beta signaling pathway / phosphatidylinositol phosphate biosynthetic process / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / positive regulation of phosphoprotein phosphatase activity / CDC42 GTPase cycle / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / PI3K events in ERBB2 signaling / RHOG GTPase cycle / T cell differentiation / RET signaling / extrinsic apoptotic signaling pathway via death domain receptors / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / positive regulation of lamellipodium assembly / : / phosphatidylinositol 3-kinase binding
Similarity search - Function
Platelet-derived growth factor receptor beta / 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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Rho GTPase-activating protein domain ...Platelet-derived growth factor receptor beta / 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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / SHC Adaptor Protein / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Platelet-derived growth factor receptor beta / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsNolte, R.T. / Eck, M.J. / Schlessinger, J. / Shoelson, S.E. / Harrison, S.C.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Crystal Structure of the Pi 3-Kinase P85 Amino- Terminal Sh2 Domain and its Phosphopeptide Complexes
Authors: Nolte, R.T. / Eck, M.J. / Schlessinger, J. / Shoelson, S.E. / Harrison, S.C.
History
DepositionJun 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Apr 28, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / reflns / struct_conn
Item: _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs ..._refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_sigma_F / _reflns.observed_criterion_sigma_I / _reflns.pdbx_redundancy / _struct_conn.pdbx_leaving_atom_flag

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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: Phosphatidylinositol 3-kinase regulatory subunit alpha
C: Platelet-derived growth factor receptor beta
D: Platelet-derived growth factor receptor beta


Theoretical massNumber of molelcules
Total (without water)30,6644
Polymers30,6644
Non-polymers00
Water2,108117
1
A: Phosphatidylinositol 3-kinase regulatory subunit alpha
C: Platelet-derived growth factor receptor beta


Theoretical massNumber of molelcules
Total (without water)15,3322
Polymers15,3322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
D: Platelet-derived growth factor receptor beta


Theoretical massNumber of molelcules
Total (without water)15,3322
Polymers15,3322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.760, 61.940, 108.360
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 regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 13939.569 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SH2 DOMAIN, RESIDUES 321-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27986
#2: Protein/peptide Platelet-derived growth factor receptor beta / PDGFR-beta / Beta platelet-derived growth factor receptor / Beta-type platelet-derived growth ...PDGFR-beta / Beta platelet-derived growth factor receptor / Beta-type platelet-derived growth factor receptor / CD140 antigen-like family member B / Platelet-derived growth factor receptor 1 / PDGFR-1


Mass: 1392.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P09619, receptor protein-tyrosine kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growDetails: 0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM ACETATE, 30% PEG4000

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 12930 / % possible obs: 98.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.37
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.92 / % possible all: 99

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.4→15 Å / Rfactor Rfree: 0.2484 / Rfactor Rwork: 0.1784 / Rfactor obs: 0.1784 / Cross valid method: THROUGHOUT
Details: THIS COODINATES FILE WAS DEPOSITED 10 YEARS AFTER THE PUBLICATION OF THE WORK. SOME OF THE DATA ARE MISSING AND ARE SHOWN AS '00000'.
Displacement parametersBiso mean: 33.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 117 2087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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