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- PDB-9eh9: Crystal structure of unbound N-SH2 domain of SHP2 -

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Basic information

Entry
Database: PDB / ID: 9eh9
TitleCrystal structure of unbound N-SH2 domain of SHP2
ComponentsIsoform 1 of Tyrosine-protein phosphatase non-receptor type 11
KeywordsPROTEIN BINDING / SHP2 / phosphatase / SH2 / allostery
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 / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / 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 / 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 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / Signal regulatory protein family interactions / face morphogenesis / ERBB 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 / 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 / Regulation of IFNA/IFNB signaling / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / 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 / 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 / hormone-mediated signaling pathway / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling / Downstream signal transduction / homeostasis of number of cells within a tissue / positive regulation of mitotic cell cycle / axonogenesis / protein tyrosine phosphatase activity / positive regulation of interferon-beta production / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / DNA damage checkpoint signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / integrin-mediated signaling pathway / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / cellular response to mechanical stimulus / Signaling by SCF-KIT
Similarity search - Function
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 / 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. ...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 / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
ACETIC ACID / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 ligand free N-SH2 domain of SHP2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2682
Polymers12,2081
Non-polymers601
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.464, 60.464, 78.293
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-315-

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 (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.93 Å3/Da / Density % sol: 58.03 %
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; 500 nL of 1.0 M sodium malonate pH 5.0, 0.1 M sodium acetate trihydrate pH 4.5, and 2% w/v polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.83→42.75 Å / Num. obs: 13292 / % possible obs: 99.49 % / Redundancy: 15 % / Biso Wilson estimate: 49.86 Å2 / CC1/2: 1 / Net I/σ(I): 26
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 1420 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5015refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→42.75 Å / SU ML: 0.3363 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 1328 9.99 %
Rwork0.2295 11963 -
obs0.2322 13291 99.48 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.69 Å2
Refinement stepCycle: LAST / Resolution: 1.83→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 4 21 836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049833
X-RAY DIFFRACTIONf_angle_d0.81341125
X-RAY DIFFRACTIONf_chiral_restr0.0516118
X-RAY DIFFRACTIONf_plane_restr0.0066148
X-RAY DIFFRACTIONf_dihedral_angle_d20.3255306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90.52371420.45121278X-RAY DIFFRACTION97.73
1.9-1.990.40371420.36751281X-RAY DIFFRACTION99.37
1.99-2.090.33531440.29631300X-RAY DIFFRACTION99.45
2.09-2.230.33971460.29011311X-RAY DIFFRACTION99.45
2.23-2.40.31991450.28191310X-RAY DIFFRACTION99.66
2.4-2.640.27761470.2641329X-RAY DIFFRACTION99.93
2.64-3.020.33111490.28161337X-RAY DIFFRACTION99.93
3.02-3.80.27481520.23221366X-RAY DIFFRACTION100
3.81-42.750.19371610.1861451X-RAY DIFFRACTION99.75
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)
13.821227926450.166766723706-3.121209131228.586605337922.735048935884.96546435168-0.7714180813320.1015643515020.753013764988-1.426086559440.663239176269-0.7612841795070.6064916969941.034750110690.09598214334550.58055771117-0.1181797612570.08635377274990.5271670202940.03393324660110.521773194564-3.1940408686525.6774399859-7.23677411617
26.8788702712-3.54792168927-0.231105151337.524934122291.907488418032.0548450686-0.147265410694-0.602702970325-0.06264841936190.9416570419770.146140172583-0.4040299207190.1452443440480.6183699376910.05221600630160.59229500621-0.0334594881598-0.01185433889160.4635724948080.02729060607290.387333226788-9.1609992461727.33429138861.06585303056
33.93106841936-3.89492712243-2.122345712983.964522851842.372961844582.565910197021.855452050030.00261458397626-0.5500485490161.27563713268-0.576156226591-1.16098555986-0.005429312821561.76387912401-2.018695517511.620989987280.165165302284-0.04420921064480.9947998348650.2604424634881.0238815569-1.02076929112.1422846379-1.47600993059
44.68476331448-2.02668695423-0.9113756384552.664674588081.178092331438.0173098683-0.184788854944-0.560190971966-0.112450728880.86224203108-0.1320110103480.4408468400510.814708991680.2284905187920.3722275557740.721317244831-0.03225341422270.08294910266970.3808792752380.01193508969240.449911777212-12.927053482920.24470827260.240412384459
56.09026303395-2.92103773914-2.236833728078.192362508733.423282860225.415340873810.0132064100861-0.345850283562-0.5408491729560.561850348204-0.2351205630390.6174750183740.2400375134260.08906938425550.1740826305140.5198671707090.02402387812930.02464635909680.4585908458650.00662180797950.513740200262-15.756168936514.5015888811-9.8052622526
63.8170316652-0.7279054247033.130994209052.569900791851.141406858053.81001899597-0.763940801104-0.2023187708752.6942527374-1.42027974274-0.28258092598-0.627829695268-1.108226700040.2541984136050.7613889209520.5847008023130.0574769162049-0.05222491881970.595831704460.03340371043560.829551983141-11.923357669630.2674941645-6.8165838865
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 12 )4 - 121 - 9
22chain 'A' and (resid 13 through 33 )13 - 3310 - 30
33chain 'A' and (resid 34 through 40 )34 - 4031 - 37
44chain 'A' and (resid 41 through 56 )41 - 5638 - 53
55chain 'A' and (resid 57 through 98 )57 - 9854 - 95
66chain 'A' and (resid 99 through 104 )99 - 10496 - 101

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