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- PDB-9ehd: Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine ... -

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Basic information

Entry
Database: PDB / ID: 9ehd
TitleCrystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD
Components
  • Isoform 1 of Tyrosine-protein phosphatase non-receptor type 11
  • Phosphorylated peptide from GRB2-associated-binding protein 1
KeywordsPROTEIN BINDING / SHP2 / phosphatase / SH2 / allostery / phosphotyrosine / activation / GAB1
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 / MET receptor recycling / positive regulation of hormone secretion / 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 / face morphogenesis / ERBB signaling pathway / vascular endothelial growth factor signaling pathway / platelet formation / triglyceride metabolic process / megakaryocyte development / organ growth / Interleukin-20 family signaling / negative regulation of type I interferon production / Interleukin-6 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR3 / 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 / positive regulation of intracellular signal transduction / Regulation of IFNA/IFNB signaling / phosphoprotein phosphatase activity / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K events in ERBB2 signaling / PI3K Cascade / positive regulation of blood vessel endothelial cell migration / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / GAB1 signalosome / 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / 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 / homeostasis of number of cells within a tissue / positive regulation of mitotic cell cycle / 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 / PH 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. ...GRB2-associated-binding protein 1-4-like / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PH 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPadua, R.A.P. / Glaser, A. / Ojoawo, A. / Kern, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: To Be Published
Title: Crystal structure of N-SH2 domain of SHP2 bound to phosphotyrosine
Authors: Padua, R.A.P. / Glaser, A. / Ojoawo, A. / Kern, D.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,5102
Polymers13,5102
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-14 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.530, 61.530, 73.445
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-210-

HOH

21A-224-

HOH

31A-226-

HOH

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Components

#1: Protein Isoform 1 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: 12207.649 Da / Num. of mol.: 1 / Fragment: N-terminal SH2 domain
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 Phosphorylated peptide from GRB2-associated-binding protein 1 / GRB2-associated binder 1 / Growth factor receptor bound protein 2-associated protein 1


Mass: 1302.278 Da / Num. of mol.: 1 / Fragment: residues 624-633 (Uniprot Isoform 1 numbering) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13480
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP, with GAB1 (QVEpYLDLDLD) 1:1.05 molar ratio; 500 nL of 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, ...Details: 500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP, with GAB1 (QVEpYLDLDLD) 1:1.05 molar ratio; 500 nL of 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, and 25% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0005 Å / Relative weight: 1
ReflectionResolution: 1.59→37.43 Å / Num. obs: 19583 / % possible obs: 99.94 % / Redundancy: 25.9 % / Biso Wilson estimate: 34.77 Å2 / CC1/2: 1 / Net I/σ(I): 15.98
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 27.1 % / Num. unique obs: 1369 / CC1/2: 0.415 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5015refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→37.43 Å / SU ML: 0.2317 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 1956 9.99 %
Rwork0.2009 17615 -
obs0.2046 19571 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.88 Å2
Refinement stepCycle: LAST / Resolution: 1.59→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 41 931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0101925
X-RAY DIFFRACTIONf_angle_d1.27791257
X-RAY DIFFRACTIONf_chiral_restr0.0571133
X-RAY DIFFRACTIONf_plane_restr0.0123166
X-RAY DIFFRACTIONf_dihedral_angle_d18.2653340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.29891370.30931230X-RAY DIFFRACTION99.85
1.63-1.670.30691380.28681242X-RAY DIFFRACTION100
1.67-1.720.30231360.28541221X-RAY DIFFRACTION100
1.72-1.780.37941370.33361242X-RAY DIFFRACTION99.93
1.78-1.840.42041380.36711231X-RAY DIFFRACTION99.93
1.84-1.920.32511380.2991241X-RAY DIFFRACTION99.93
1.92-20.31451370.23441231X-RAY DIFFRACTION100
2-2.110.27331390.21191254X-RAY DIFFRACTION100
2.11-2.240.27041380.23031250X-RAY DIFFRACTION99.86
2.24-2.410.23441390.21011253X-RAY DIFFRACTION100
2.41-2.660.24281410.20021267X-RAY DIFFRACTION100
2.66-3.040.26441400.21191270X-RAY DIFFRACTION99.93
3.04-3.830.23211450.17661301X-RAY DIFFRACTION100
3.83-37.430.19221530.1721382X-RAY DIFFRACTION99.74
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)
12.769255094822.898428236822.558924550873.319884314412.94312544063.8470230578-0.8979093896490.314783289168-0.466616195543-0.1814565005880.985367332129-0.247828445864-1.290792296070.967956681641-0.1203160683590.446328971710.0671722193240.08106493191450.494737327405-0.08399738684570.463534888849-4.0182065895125.2573920541-4.52443466336
20.8057404395310.220021412104-0.6060697399061.634052136051.220742532841.5976651519-0.0790353240338-0.43801773656-0.1362679380950.4596440256250.057974276196-0.2178321184750.8502724717140.383703914757-0.00423596149060.5556569833680.1063380919740.03016020405190.381119613631-0.03067916384670.339713204039-10.622593751428.06295229512.27532501288
30.9789960101271.250188742250.4723080458571.56869444412-0.02782759891140.467561144872-0.287293527009-0.320330897744-0.3492061504820.3965340232460.1347626866090.07864402578830.8567891384760.324223465532-0.1149920496110.8132372155610.1991300837320.1673980756250.3951811884870.0494682220420.383713893173-9.2221971302617.77266468690.228685630574
40.6776628478470.8787903834050.3319996489411.766985589830.6285721107910.424492641845-0.843121009747-0.583189349183-0.5899736082571.347041258480.08361591592861.400381962341.2839987382-0.0864078572129-0.2447223870060.7435308891820.1119789425540.2403451219440.3540672115010.01829060541290.380788416558-15.550636805820.38120032552.59552173025
5-0.04754908698260.0629553567921-0.4483071621861.042856052770.2260066293051.19902315669-0.1309627462540.195112993692-0.3341567259690.314175962459-0.02377981779710.1577890487160.4243959215080.141825420398-0.00509081347640.4178375475920.03989806648510.1326414553020.2855209860060.03200827616110.396441997987-11.89457563089.81649150121-11.0747578029
60.303288658093-0.294997280848-0.2642740057260.2337084108060.01800270887240.2399308829720.04574187168790.2712669079760.2969234611160.210504118504-0.01635283053430.546795067977-0.407979657374-0.3520449167690.0001187009869670.3795714937450.06527918007240.08800272355910.3176119686040.04958093888020.389463851541-15.841613738820.1127917874-13.2509724505
70.7053237964440.02800489239470.8888215933721.63761095099-0.09494851799641.367524773380.402921686405-0.2892939971170.622487285781.169557153250.5240096717091.32295155007-0.568439830769-1.61436482135-0.2612832293550.5986511094630.06631913220070.4119122785470.6002462164570.01379942415010.922284550278-24.932312055316.9309711231-3.67154234691
82.06480063464-0.06978157300772.429930718460.0287781020645-0.1141694617462.91396057003-0.826073992778-0.355265288433-0.2600743579590.701553975792-0.01857123000511.912747507660.0837073596842-1.68506386118-1.366720602880.602657788954-0.07920722185240.4178008086160.624983821803-0.1369284227891.01542665698-25.255522269720.5669005041-0.677842989031
90.720432307518-0.06417468974770.2452590891520.0558245757810.04550720820090.6490002893560.3655528426560.074330037164-0.2823788999140.355620014541-0.2471196605820.112363882190.5538807485540.4584235887160.01658092034490.393406659417-0.02271319918870.03277481067170.332934450415-0.06179680257660.393486982601-12.958593918230.2737972522-5.84744501168
102.36321788052-0.6864697048810.2290021838990.7240375893690.6358821447021.58596927906-0.0774703017445-0.497131212837-1.021997081781.548605008-0.04016129511090.9631157259941.370609874560.001100384515540.08752231894031.136369271740.1075476662320.3424255762030.5466485122890.08194859751820.531666588853-16.714749596212.97945486042.57659555625
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 12 )AA5 - 121 - 8
22chain 'A' and (resid 13 through 33 )AA13 - 339 - 29
33chain 'A' and (resid 34 through 47 )AA34 - 4730 - 43
44chain 'A' and (resid 48 through 56 )AA48 - 5644 - 52
55chain 'A' and (resid 57 through 73 )AA57 - 7353 - 69
66chain 'A' and (resid 74 through 83 )AA74 - 8370 - 79
77chain 'A' and (resid 84 through 92 )AA84 - 9280 - 88
88chain 'A' and (resid 93 through 97 )AA93 - 9789 - 93
99chain 'A' and (resid 98 through 104 )AA98 - 10494 - 100
1010chain 'B' and (resid 2 through 11 )BB2 - 111 - 10

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