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- PDB-9eic: Crystal structure of unbound N-SH2 domain of SHP2 with T42A mutation -

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Basic information

Entry
Database: PDB / ID: 9eic
TitleCrystal structure of unbound N-SH2 domain of SHP2 with T42A mutation
ComponentsIsoform 1 of Tyrosine-protein phosphatase non-receptor type 11
KeywordsPROTEIN BINDING / SHP2 / phosphatase / SH2 / allostery / phosphotyrosine / activation
Function / homology
Function and homology information


atrioventricular canal development / genitalia development / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / negative regulation of neutrophil activation / negative regulation of chondrocyte differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / face morphogenesis / Interleukin-37 signaling ...atrioventricular canal development / genitalia development / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / negative regulation of neutrophil activation / negative regulation of chondrocyte differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / face morphogenesis / Interleukin-37 signaling / positive regulation of ossification / Signaling by Leptin / negative regulation of cell adhesion mediated by integrin / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / Signal regulatory protein family interactions / ERBB signaling pathway / Interleukin-20 family signaling / Interleukin-6 signaling / Co-inhibition by CTLA4 / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / Platelet sensitization by LDL / negative regulation of T cell activation / inner ear development / fibroblast growth factor receptor signaling pathway / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / peptide hormone receptor binding / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / negative regulation of type I interferon production / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / Prolactin receptor signaling / PECAM1 interactions / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / positive regulation of intracellular signal transduction / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Co-inhibition by PD-1 / PI3K Cascade / ephrin receptor signaling pathway / positive regulation of insulin receptor signaling pathway / regulation of protein-containing complex assembly / negative regulation of T cell receptor signaling pathway / negative regulation of T cell proliferation / Regulation of IFNG signaling / GAB1 signalosome / T cell costimulation / Activated NTRK2 signals through FRS2 and FRS3 / GPVI-mediated activation cascade / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / phosphotyrosine residue binding / Signaling by FLT3 ITD and TKD mutants / phosphoprotein phosphatase activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-tyrosine-phosphatase / FRS-mediated FGFR1 signaling / Tie2 Signaling / positive regulation of D-glucose import across plasma membrane / protein tyrosine phosphatase activity / FLT3 Signaling / cell adhesion molecule binding / positive regulation of interferon-beta production / Downstream signal transduction / cellular response to epidermal growth factor stimulus / protein tyrosine kinase binding / insulin receptor binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / brain development / Negative regulation of FGFR3 signaling / cellular response to mechanical stimulus / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Signaling by SCF-KIT / Spry regulation of FGF signaling / receptor tyrosine kinase binding / vasodilation / epidermal growth factor receptor signaling pathway / cytokine-mediated signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / heart development / Signaling by CSF1 (M-CSF) in myeloid cells / Interferon alpha/beta signaling / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / signaling receptor complex adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / cadherin binding / focal adhesion / nucleolus
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
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling.
Authors: Glaser, A.W. / Padua, R.A.P. / Ojoawo, A.M. / Sullivan, C. / 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 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)12,4634
Polymers12,1781
Non-polymers2853
Water81145
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)56.723, 56.723, 80.332
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-338-

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: 12177.623 Da / Num. of mol.: 1 / Fragment: N-terminal SH2 domain / Mutation: T42A
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
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 500 nL of 0.1 M Tris hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.58→35.89 Å / Num. obs: 18599 / % possible obs: 99.97 % / Redundancy: 11.6 % / Biso Wilson estimate: 28.62 Å2 / CC1/2: 1 / Net I/σ(I): 6.5
Reflection shellResolution: 1.58→1.62 Å / Num. unique obs: 1392 / CC1/2: 0.3 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→35.89 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2551
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 1860 10 %
Rwork0.2048 16739 -
obs0.2063 18599 99.97 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.56 Å2
Refinement stepCycle: LAST / Resolution: 1.58→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 15 45 875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126904
X-RAY DIFFRACTIONf_angle_d1.07951232
X-RAY DIFFRACTIONf_chiral_restr0.062123
X-RAY DIFFRACTIONf_plane_restr0.0096165
X-RAY DIFFRACTIONf_dihedral_angle_d16.6071331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.34821400.35061252X-RAY DIFFRACTION99.71
1.62-1.670.33791410.30441275X-RAY DIFFRACTION100
1.67-1.720.28241390.26621248X-RAY DIFFRACTION99.93
1.72-1.790.30111400.25021271X-RAY DIFFRACTION100
1.79-1.860.27421400.25791248X-RAY DIFFRACTION100
1.86-1.940.27311390.22831257X-RAY DIFFRACTION100
1.94-2.040.1811430.19821285X-RAY DIFFRACTION100
2.04-2.170.20811410.18221278X-RAY DIFFRACTION100
2.17-2.340.22441430.19131283X-RAY DIFFRACTION100
2.34-2.580.20171440.1941300X-RAY DIFFRACTION100
2.58-2.950.24611440.21321291X-RAY DIFFRACTION100
2.95-3.710.19691480.18761332X-RAY DIFFRACTION100
3.71-35.890.20251580.20061419X-RAY DIFFRACTION100
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)
16.568558142651.24607302671-1.20531598893.59756830424-3.750102364314.04822391067-0.477539464816-0.270442477291-0.673604492696-0.216868395540.602788793730.7072044813221.17138807115-0.840013454124-0.1040290532830.487809509365-0.0395459485578-0.05385210389820.4399040117750.07990705414540.5505495043-24.77850852834.06104242817-9.98351001905
23.528658694830.4147827769481.440823134214.06637945182-3.184409450284.49675924949-0.0147119767805-0.394445742761-0.1011776705290.4382145522670.2604127661120.557207923139-0.299520575603-0.652267160511-0.1540510016120.2244381017350.0242838291920.03815410076490.2127819916820.02907616784860.23854115704-20.14701629233.31744596678-0.352588785002
35.808446298592.9586508164.126077488793.30614266290.6475160602424.10664859798-1.21614159174-2.24773176092-0.1170243058162.92887947858-0.231532321162.587945138670.67528482082-1.001156945611.330552279161.108921952740.3612879075510.3663646762930.9314877838040.01538926179461.09566841584-31.930351552115.4365223361-3.911745563
44.21987484647-0.4609726330543.876039104063.7362279111-4.155051278758.37498153582-0.385529466103-0.706602504553-0.02263769567590.5688879976540.159960083858-0.03589355156-0.625462653027-0.05120001527810.1282714138370.3879351246720.010753000026-0.04120479096770.241769755518-0.04416653096580.254155428-18.03204587549.6462463688-2.05535380654
59.21096471013-4.95925078154.363752526524.63127768504-4.113714958583.65474927367-0.407263399564-0.2368526077770.2342914735891.278992254220.265213023374-0.0218012451518-1.195433279640.05690764174790.2094145515970.4486674316510.0340818967774-0.02092557811970.246335148684-0.011142883890.303051653516-17.488060996811.86398687542.00214600853
66.15342493745-2.422574572091.487139798845.78510608312-2.365255137799.31570148958-0.04104308554610.01304148672490.09203750508540.4496134762440.0248637544813-0.0324920190863-0.353818868582-0.09223278530690.03995672607210.3175050530280.00406063930709-0.02839607763640.212077204054-0.01627281170090.263108171708-20.285735109321.3594066783-12.2019210959
76.25663040462-1.054466657374.12570246387.4696741551-1.696270511053.23402468656-0.002378867749160.482485647513-0.367824860614-0.239176616044-0.135831780812-1.13703073103-0.2103867918620.6148982588260.1480209267730.260542352742-0.008488856608410.01867752236440.3318164838820.02921178586820.459478120968-11.255552293413.0147239125-12.6352387296
81.13868403243-1.828923320410.5837514791163.122523347-0.3865236355641.94305270036-0.393507542939-0.290187276340.7920854052610.777910036561-0.328590962967-0.0321948242653-0.406622056884-0.229484751893-0.3657455446141.05957206686-0.3183822363770.1331633916570.528879762092-0.2588854695571.00698867118-10.059270991221.4044864123-0.39945614118
92.539861323172.336284360890.5723745837684.90230570724.971624374057.30540130962-0.59384716852-0.5582661106650.9623509861870.7349843863640.234925009856-1.40837079494-1.108985130941.664068192610.09416123436790.532673596821-0.0775552926853-0.2272424597910.497266282980.04312546301460.713396350705-8.5467161568713.0487630442-3.1037243124
104.083168209340.806133690583-3.723327085934.06190311718-3.172885111155.28828609228-0.1498797145010.285597688622-0.138569020564-0.647808590295-0.05926121234650.07432126218921.112022028550.1647317138390.1986313556330.470612951611-0.00204836973927-0.02757209358490.251697742001-0.009890392066180.325977387985-15.31834075810.672281871888-7.33615010487
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 3 through 12 )3 - 121 - 10
22chain 'A' and (resid 13 through 33 )13 - 3311 - 31
33chain 'A' and (resid 34 through 40 )34 - 4032 - 38
44chain 'A' and (resid 41 through 47 )41 - 4739 - 45
55chain 'A' and (resid 48 through 55 )48 - 5546 - 53
66chain 'A' and (resid 56 through 73 )56 - 7354 - 71
77chain 'A' and (resid 74 through 88 )74 - 8872 - 86
88chain 'A' and (resid 89 through 93 )89 - 9387 - 91
99chain 'A' and (resid 94 through 98 )94 - 9892 - 96
1010chain 'A' and (resid 99 through 104 )99 - 10497 - 102

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