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- PDB-6cmq: Structure of human SHP2 without N-SH2 domain -

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Basic information

Entry
Database: PDB / ID: 6cmq
TitleStructure of human SHP2 without N-SH2 domain
ComponentsTyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE / protein tyrosine phosphatase / src homology domain 2 / open state / active mutant
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 / negative regulation of neutrophil activation / cerebellar cortex formation / positive regulation of hormone secretion / regulation of protein export from nucleus / Interleukin-37 signaling / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of ossification / Signaling by Leptin / 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 / negative regulation of type I interferon production / organ growth / Interleukin-20 family signaling / 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 / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / Regulation of IFNA/IFNB signaling / 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 / GAB1 signalosome / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / Regulation of IFNG signaling / Activated NTRK2 signals through FRS2 and FRS3 / GPVI-mediated activation cascade / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / cell adhesion molecule binding / negative regulation of T cell proliferation / T cell costimulation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / hormone-mediated signaling pathway / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling / homeostasis of number of cells within a tissue / Downstream signal transduction / 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 / 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 / Spry regulation of FGF signaling
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPadua, R.A.P. / Sun, Y. / Marko, I. / Pitsawong, W. / Kern, D.
Funding support Brazil, United States, 3items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)233809/2014-7 Brazil
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100966 United States
CitationJournal: Nat Commun / Year: 2018
Title: Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.
Authors: Padua, R.A.P. / Sun, Y. / Marko, I. / Pitsawong, W. / Stiller, J.B. / Otten, R. / Kern, D.
History
DepositionMar 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Tyrosine-protein phosphatase non-receptor type 11
C: Tyrosine-protein phosphatase non-receptor type 11
D: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)196,5264
Polymers196,5264
Non-polymers00
Water362
1
A: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)49,1311
Polymers49,1311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)49,1311
Polymers49,1311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)49,1311
Polymers49,1311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)49,1311
Polymers49,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.550, 56.200, 247.460
Angle α, β, γ (deg.)90.000, 93.990, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR(chain 'A' and (resid 107 through 108 or resid 110...AA107 - 1085 - 6
12GLUGLUTHRTHR(chain 'A' and (resid 107 through 108 or resid 110...AA110 - 1538 - 51
13SERSERCYSCYS(chain 'A' and (resid 107 through 108 or resid 110...AA165 - 17463 - 72
14TYRTYRGLUGLU(chain 'A' and (resid 107 through 108 or resid 110...AA179 - 18577 - 83
15PHEPHEASPASP(chain 'A' and (resid 107 through 108 or resid 110...AA187 - 18885 - 86
16LEULEUMETMET(chain 'A' and (resid 107 through 108 or resid 110...AA190 - 20288 - 100
17VALVALLEULEU(chain 'A' and (resid 107 through 108 or resid 110...AA209 - 236107 - 134
18VALVALGLNGLN(chain 'A' and (resid 107 through 108 or resid 110...AA243 - 256141 - 154
19TYRTYRPROPRO(chain 'A' and (resid 107 through 108 or resid 110...AA263 - 312161 - 210
110LYSLYSGLNGLN(chain 'A' and (resid 107 through 108 or resid 110...AA325 - 526223 - 424
21PROPROTHRTHR(chain 'D' and (resid 107 through 108 or resid 110...DD107 - 1085 - 6
22GLUGLUTHRTHR(chain 'D' and (resid 107 through 108 or resid 110...DD110 - 1538 - 51
23SERSERCYSCYS(chain 'D' and (resid 107 through 108 or resid 110...DD165 - 17463 - 72
24TYRTYRGLUGLU(chain 'D' and (resid 107 through 108 or resid 110...DD179 - 18577 - 83
25PHEPHEASPASP(chain 'D' and (resid 107 through 108 or resid 110...DD187 - 18885 - 86
26LEULEUMETMET(chain 'D' and (resid 107 through 108 or resid 110...DD190 - 20288 - 100
27VALVALLEULEU(chain 'D' and (resid 107 through 108 or resid 110...DD209 - 236107 - 134
28VALVALGLNGLN(chain 'D' and (resid 107 through 108 or resid 110...DD243 - 256141 - 154
29TYRTYRPROPRO(chain 'D' and (resid 107 through 108 or resid 110...DD263 - 312161 - 210
210LYSLYSGLNGLN(chain 'D' and (resid 107 through 108 or resid 110...DD325 - 526223 - 424

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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 / Shp2 / SH-PTP3


Mass: 49131.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.9→82.29 Å / Num. obs: 42597 / % possible obs: 99.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 41.56 Å2 / Rpim(I) all: 0.5172 / Net I/σ(I): 4.3
Reflection shellResolution: 2.9→3.01 Å / Redundancy: 4.7 % / Num. unique obs: 4448 / Rpim(I) all: 0.7646 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dgp

4dgp


Resolution: 2.9→82.29 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7879 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2764 1997 4.71 %
Rwork0.2491 40401 -
obs0.2504 42398 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→82.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12505 0 0 2 12507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001812773
X-RAY DIFFRACTIONf_angle_d0.444717271
X-RAY DIFFRACTIONf_chiral_restr0.04151899
X-RAY DIFFRACTIONf_plane_restr0.00292238
X-RAY DIFFRACTIONf_dihedral_angle_d7.10427660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39621520.33192853X-RAY DIFFRACTION98.72
2.97-3.050.33391260.32542846X-RAY DIFFRACTION98.74
3.05-3.140.34051490.30382882X-RAY DIFFRACTION98.63
3.14-3.240.31911380.29932800X-RAY DIFFRACTION98.39
3.24-3.360.36311400.29952887X-RAY DIFFRACTION98.47
3.36-3.490.36471430.28222886X-RAY DIFFRACTION98.09
3.49-3.650.30811420.27052830X-RAY DIFFRACTION97.86
3.65-3.850.30581430.26272847X-RAY DIFFRACTION98
3.85-4.090.25991440.24352883X-RAY DIFFRACTION98.54
4.09-4.40.26931390.22812887X-RAY DIFFRACTION98.89
4.4-4.850.21211360.19822873X-RAY DIFFRACTION98.14
4.85-5.550.1971490.20642930X-RAY DIFFRACTION98.65
5.55-6.990.25811430.23752944X-RAY DIFFRACTION98.78
6.99-82.320.20851530.20123053X-RAY DIFFRACTION99.63
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)
11.526575238041.060035033920.6679924852084.849635433212.673264470251.30213364313-0.0665751797718-0.2336988955870.355262431730.5044174453480.36214821527-0.0830047620264-2.26018130963E-60.1650672384-0.1816834700510.500584039351-0.04249793318270.04956142662850.5607789566530.006552153528960.49365133172845.869234971429.985439159740.0445029429
22.609097610870.13274766771.22454889894.402425730071.502134551824.339144450470.2137418087230.1918562261520.0750199218052-0.0437378628701-0.0107828650978-0.250903345137-0.01269565228310.2043193108980.4348703597670.0611276744417-0.03489315062070.09251685324920.277023295681-0.0057600650760.32470593076441.859609410317.381367192515.2630724633
35.24267567232-0.112944133275-0.287353863952.752145756770.08096706852277.18936740523-0.0941913644534-0.9070837785030.9014794474360.869788510663-0.09502998250980.0125601447249-0.60996991224-0.19990547672-0.4037070357850.749397735885-0.07129025785520.1384734081250.550179878022-0.1222865116340.44770539621713.15105568245.3489745425750.4714845139
42.318653609581.08147474281.029864140014.692655149281.4878757644.015003629610.09381930597620.01476129332020.03852469406980.300704166764-0.1488630572670.4280267981860.114251640147-0.109129980566-0.301444710042-0.0346883550763-0.01746873383620.158036595950.379789408473-0.01253741594520.3522309209568.43129280443-17.781021326917.6878495612
53.180781866140.938932655246-0.216664916483.117423683752.942085487579.90657073914-0.02146317052860.96576551851-0.481334264517-0.7819015439840.06643745834580.06336178378520.921685493934-0.3568146114380.08861853002520.7729730749910.0889302935646-0.04810308798730.71040965357-0.08574809392090.60338645954-28.176203520250.439223869776.7782104275
62.11748825311-2.031191399181.626389920748.397430425470.9943909836021.815341190720.195241866881.511566749880.590232309663-2.11536559909-0.259427935372-0.997009421226-0.802317959621-0.124844581928-1.372487566890.4204712847550.205444480044-0.1238258532410.450562504180.3045668793820.704057043033-32.025796016381.68596965591.0068222171
74.86200055831-0.222304192114-0.2770040971532.54783223909-0.4558346420184.81664190697-0.166725046823-0.1720283586950.641160712697-0.223707160290.03862338062660.365726857714-0.302439212876-0.259628733059-0.1460415168460.1508941589040.064977388729-0.0218332632670.3512866386980.0491827356380.531611687772-38.660749082583.7253180524106.359611858
82.760152606-0.894147821646-0.9211457766764.882538539463.276519586683.65807485617-0.0981775965291-0.251477316929-0.2717292685560.08063451644380.01418805067360.2644334508330.322661359037-0.258604699699-0.2053693765520.06126012989820.0651304684509-0.01566135850570.4352798624190.09999166549210.372976499002-34.704962449570.5308229461110.021208462
91.617548381560.253840441440.05548180080872.867129950731.486971083615.58226960502-0.2557279991550.453241237707-0.167117642551-0.6887718864230.5262320726990.09925208914330.4828106030970.3014820516770.7275293983030.4355707377590.03093223914230.1049750519260.610022275959-0.07835271185360.4240418716768.9555318131214.161413508979.378352803
102.990096300850.19374416158-0.1117183530913.78544864842-1.663053728794.524022224790.169452874123-0.1810195729370.371094207971-0.0749994554986-0.0971818307274-0.0266144739480.01917632770340.16325009374-0.4614484742820.0529324447162-0.03184306392060.03191940173920.305652649284-0.0624978388780.440905252242-4.5521940608746.0756369823107.187818486
115.17321117743-1.782706048871.147333852495.919944116141.724935774633.678208588680.0469277343767-0.149707458488-0.65453473694-0.1294430890280.2289445578250.2304654692790.2509627677950.08972450472230.03067616804090.223285882640.03811851378610.07023499462550.317460717112-0.03330013762960.4087552090212.4886813885427.933216074999.1613198882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 106 through 326 )
2X-RAY DIFFRACTION2chain 'A' and (resid 327 through 528 )
3X-RAY DIFFRACTION3chain 'B' and (resid 107 through 219 )
4X-RAY DIFFRACTION4chain 'B' and (resid 220 through 528 )
5X-RAY DIFFRACTION5chain 'C' and (resid 107 through 246 )
6X-RAY DIFFRACTION6chain 'C' and (resid 247 through 276 )
7X-RAY DIFFRACTION7chain 'C' and (resid 277 through 365 )
8X-RAY DIFFRACTION8chain 'C' and (resid 366 through 528 )
9X-RAY DIFFRACTION9chain 'D' and (resid 106 through 256 )
10X-RAY DIFFRACTION10chain 'D' and (resid 257 through 463 )
11X-RAY DIFFRACTION11chain 'D' and (resid 464 through 527 )

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