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- PDB-9qa5: Structure of the N-SH2 domain of SHP2 in complex with the phospho... -

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Basic information

Entry
Database: PDB / ID: 9qa5
TitleStructure of the N-SH2 domain of SHP2 in complex with the phosphoY627-Gab1 (613-651) peptide
Components
  • GRB2-associated-binding protein 1
  • Isoform 3 of Tyrosine-protein phosphatase non-receptor type 11
KeywordsSIGNALING PROTEIN / SH2-domain / phosphatase / PTPN11 / phospho-tyrosine
Function / homology
Function and homology information


negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / endothelial cell chemotaxis / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / endothelial cell chemotaxis / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / Activated NTRK2 signals through PI3K / positive regulation of hormone secretion / MET receptor recycling / regulation of protein export from nucleus / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / Signaling by Leptin / positive regulation of ossification / MET activates PTPN11 / hormone metabolic process / MET activates RAP1 and RAC1 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / ERBB signaling pathway / face morphogenesis / platelet formation / vascular endothelial growth factor signaling pathway / triglyceride metabolic process / organ growth / megakaryocyte development / Interleukin-20 family signaling / negative regulation of type I interferon production / Interleukin-6 signaling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / peptide hormone receptor binding / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / phosphoprotein phosphatase activity / Regulation of IFNA/IFNB signaling / positive regulation of intracellular signal transduction / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / PI3K events in ERBB2 signaling / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / positive regulation of insulin receptor signaling pathway / GAB1 signalosome / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / Regulation of IFNG signaling / Activated NTRK2 signals through FRS2 and FRS3 / Signaling by FGFR4 in disease / GPVI-mediated activation cascade / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / negative regulation of T cell proliferation / cell adhesion molecule binding / Signaling by FLT3 ITD and TKD mutants / T cell costimulation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / hormone-mediated signaling pathway / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling / Signaling by FGFR1 in disease / signaling adaptor activity / Downstream signal transduction / positive regulation of mitotic cell cycle / homeostasis of number of cells within a tissue / axonogenesis / protein tyrosine phosphatase activity
Similarity search - Function
GRB2-associated-binding protein 1-4-like / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / PH domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...GRB2-associated-binding protein 1-4-like / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / PH domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11 / GRB2-associated-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMachner, L. / Breithaupt, C. / Kniest, J. / Parthier, C. / Feller, S.M. / Stubbs, M.T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Structure / Year: 2025
Title: Mechanism of SHP2 activation by bis-Tyr-phosphorylated Gab1
Authors: Machner, L. / Shaikhqasem, A. / Gruber, T. / Hamdi, F. / Breithaupt, C. / Kniest, J. / Wiebe, F. / Lewitzky, M. / Parthier, C. / Kyrilis, F.L. / Balbach, J. / Kastritis, P.L. / Feller, S.M. / Stubbs, M.T.
History
DepositionFeb 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Tyrosine-protein phosphatase non-receptor type 11
B: GRB2-associated-binding protein 1


Theoretical massNumber of molelcules
Total (without water)16,2302
Polymers16,2302
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-17 kcal/mol
Surface area5860 Å2
Unit cell
Length a, b, c (Å)60.780, 60.780, 69.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

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Components

#1: Protein Isoform 3 of Tyrosine-protein phosphatase non-receptor type 11 / Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP- ...Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP-2 / Shp2 / SH-PTP3


Mass: 12006.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide GRB2-associated-binding protein 1 / GRB2-associated binder 1 / Growth factor receptor bound protein 2-associated protein 1


Mass: 4223.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13480
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5 % PEG3350, 0.2 M NaCl, 0.1 M BisTris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Jan 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→69.85 Å / Num. obs: 8364 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 31.76 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.137 / Net I/σ(I): 14
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 633 / CC1/2: 0.817 / Rrim(I) all: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→27.87 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2729 405 4.88 %
Rwork0.2258 7890 -
obs0.2281 8295 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.2 Å2
Refinement stepCycle: LAST / Resolution: 2.08→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 43 913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061898
X-RAY DIFFRACTIONf_angle_d0.95021218
X-RAY DIFFRACTIONf_chiral_restr0.0499130
X-RAY DIFFRACTIONf_plane_restr0.0071158
X-RAY DIFFRACTIONf_dihedral_angle_d15.794337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.380.31811420.24622569X-RAY DIFFRACTION100
2.38-30.37411270.28042591X-RAY DIFFRACTION99.74
3-27.870.23281360.20212730X-RAY DIFFRACTION99.38

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