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- PDB-4qsy: SHP2 SH2 domain in complex with GAB1 peptide -

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Basic information

Entry
Database: PDB / ID: 4qsy
TitleSHP2 SH2 domain in complex with GAB1 peptide
Components
  • GRB2-associated-binding protein 1
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE/PROTEIN BINDING / SH2 domain / signalling / PTR binding / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


endothelial cell chemotaxis to vascular endothelial growth factor / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / : / Signaling by FGFR3 fusions in cancer / response to hepatocyte growth factor / : / : / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization ...endothelial cell chemotaxis to vascular endothelial growth factor / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / : / Signaling by FGFR3 fusions in cancer / response to hepatocyte growth factor / : / : / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / ERBB2 signaling pathway / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion / cerebellar cortex formation / Activated NTRK2 signals through PI3K / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / MET receptor recycling / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / negative regulation of chondrocyte differentiation / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / MET activates RAP1 and RAC1 / face morphogenesis / ERBB signaling pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / vascular endothelial growth factor signaling pathway / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / CTLA4 inhibitory signaling / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / PECAM1 interactions / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / PI3K events in ERBB2 signaling / non-membrane spanning protein tyrosine phosphatase activity / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / PD-1 signaling / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / Regulation of IFNG signaling / Signaling by FGFR4 in disease / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Tie2 Signaling / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / GPVI-mediated activation cascade / Signaling by FGFR2 in disease / T cell costimulation / FLT3 Signaling / Signaling by FGFR1 in disease / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / PH domain / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / 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 / 2-Layer Sandwich / Alpha Beta
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: 2.1 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: To be Published
Title: Selective targeting of GAB adapter protein SHP2 tyrosine phosphatase interaction attenuates ERK signaling
Authors: Gogl, G. / Remenyi, A.
History
DepositionJul 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,7542
Polymers13,7542
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-15 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.780, 61.780, 74.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

21A-217-

HOH

31A-234-

HOH

41A-252-

HOH

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Components

#1: Protein 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: 12150.598 Da / Num. of mol.: 1 / Fragment: SH2 domain, UNP residues 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli (E. coli) / 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: 1603.598 Da / Num. of mol.: 1 / Fragment: phospho peptide, UNP residues 621-633 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13480
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 17, 2012
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→43.69 Å / Num. all: 8894 / Num. obs: 8862 / % possible obs: 99.6 % / Observed criterion σ(F): 2.77 / Observed criterion σ(I): 2.77
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.77 / Num. measured obs: 1689 / Num. possible: 634 / Num. unique obs: 623 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYD

1ayd


Resolution: 2.1→43.685 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 422 4.78 %RANDOM
Rwork0.2 ---
obs0.2014 8822 99.67 %-
all-8894 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 53 948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004930
X-RAY DIFFRACTIONf_angle_d0.8291264
X-RAY DIFFRACTIONf_dihedral_angle_d15.969343
X-RAY DIFFRACTIONf_chiral_restr0.033134
X-RAY DIFFRACTIONf_plane_restr0.003167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.40390.30761380.23662720
2.4039-3.02850.30711430.24062762
3.0285-43.69450.18841410.17772918
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)
12.55252.5068-1.66886.83492.27825.7282-0.4854-0.35450.29640.09270.7871-0.2465-0.53342.3497-0.21850.46140.09570.00280.4962-0.13380.5272-4.043225.2865-4.8412
29.4985-5.91993.20174.228-1.32282.8046-0.6545-0.60420.50351.0380.6086-1.36460.84420.6389-0.05720.61660.1458-0.01980.4514-0.06960.4172-8.801829.7394.9929
31.0111.641-0.28713.4664-0.46093.8269-0.2063-0.20530.0013-0.0420.1016-0.7020.75940.58650.16080.49980.1220.05480.3621-0.010.264-10.716921.5435-0.8301
40.47370.4929-0.70473.80944.36888.8442-0.9466-0.6521-0.4941.30420.36880.71011.29290.27540.7580.61250.10450.21330.35670.02960.3593-15.397220.74462.2917
54.662-0.501-2.796.3161.09564.6548-0.21860.0514-0.11810.62150.16790.35630.1704-0.03290.11120.36560.01170.08560.23690.05170.315-12.092210.0683-11.2653
62.3661-2.65940.69225.93582.21324.32830.1864-0.41770.3090.3349-0.18820.8556-0.4067-0.6556-0.05290.34610.03070.05060.32180.01460.3982-18.411420.3071-12.1393
73.31372.5732-2.06646.87173.59686.9624-0.5839-0.8619-0.29091.708-0.45461.11710.8969-1.10510.98120.8948-0.00750.29520.91230.00170.8552-26.533214.16382.0927
82.00966.83221.89444.60411.15352.4094-0.4543-0.27970.05520.89470.14770.7148-0.0822-1.07960.32410.49580.03230.28620.5019-0.02550.5174-23.53422.0161-2.2987
93.1436-0.63030.31128.9663-0.62522.9826-0.0232-0.2240.5740.8292-0.2944-0.11940.47650.51030.23980.3086-0.05640.04640.3524-0.09260.4033-12.344231.494-6.1238
102.99343.81913.84536.68294.46799.31920.0812-0.5499-0.81391.33370.10680.36680.7397-0.7607-0.22420.86380.04540.19310.52310.11150.5428-15.788313.90363.3432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 47 )
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 56 )
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 88 )
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 93 )
8X-RAY DIFFRACTION8chain 'A' and (resid 94 through 98 )
9X-RAY DIFFRACTION9chain 'A' and (resid 99 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 11 )

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