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- PDB-9mq5: Crystal structure SHP2 tandem SH2 domains in complex with PZR dou... -

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Basic information

Entry
Database: PDB / ID: 9mq5
TitleCrystal structure SHP2 tandem SH2 domains in complex with PZR doubly tyrosine phosphorylated ITIM peptide
Components
  • Myelin protein zero-like protein 1
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsSIGNALING PROTEIN / SH2 domain / phosphotyrosine / ITIM / complex
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 / positive regulation of hormone secretion / negative regulation of neutrophil activation / regulation of protein export from nucleus / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of ossification / Interleukin-37 signaling / Signaling by Leptin / hormone metabolic process / MET activates PTPN11 / 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 / negative regulation of type I interferon production / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / peptide hormone receptor binding / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / platelet-derived growth factor receptor signaling pathway / MAPK1 (ERK2) activation / PECAM1 interactions / inner ear development / Bergmann glial cell differentiation / peptidyl-tyrosine dephosphorylation / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / RET signaling / Regulation of IFNA/IFNB signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / Co-inhibition by PD-1 / non-membrane spanning protein tyrosine phosphatase activity / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / Activated NTRK2 signals through FRS2 and FRS3 / Regulation of IFNG signaling / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / Signaling by FLT3 ITD and TKD mutants / T cell costimulation / negative regulation of T cell proliferation / FRS-mediated FGFR2 signaling / hormone-mediated signaling pathway / cell adhesion molecule binding / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / FLT3 Signaling / protein-tyrosine-phosphatase / homeostasis of number of cells within a tissue / axonogenesis / Downstream signal transduction / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / positive regulation of interferon-beta production / protein tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / 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 / negative regulation of insulin secretion
Similarity search - Function
Myelin P0 protein-related / 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 ...Myelin P0 protein-related / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH2 domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Myelin protein zero-like protein 1 / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStiegler, A.L. / Boggon, T.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: SHP2 genetic variants in NSML-associated RASopathies disrupt PZR-IRX transcription factor signaling axis
Authors: Perla, S. / Stiegler, A.L. / Yi, J.-S. / Enyenihi, L. / Zhang, L. / Riaz, M. / An, E. / Qyang, Y. / Boggon, T.J. / Bennett, A.M.
History
DepositionJan 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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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: Myelin protein zero-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4689
Polymers29,0332
Non-polymers4347
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.960, 30.130, 115.690
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number5
Space group name H-MC121

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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: 25230.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide Myelin protein zero-like protein 1 / Protein zero-related


Mass: 3802.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95297
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.06 Å3/Da / Density % sol: 40.28 % / Description: Rod-shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% w/v Polyethylene glycol 3,350, 0.1 M Lithium Acetate, 0.1 M Bis-Tris pH 6.5
Temp details: ambient temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2024
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.7→34.31 Å / Num. obs: 26508 / % possible obs: 99.7 % / Redundancy: 17.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.031 / Rrim(I) all: 0.131 / Net I/σ(I): 12.06
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.761.58726130.7381.6331
1.76-1.831.16125670.8631.1961
1.83-1.910.81225230.9150.8371
1.91-2.020.56128720.9640.5771
2.02-2.140.35125230.9830.3621
2.14-2.310.26226790.9910.271
2.31-2.540.19526120.9940.21
2.54-2.910.14926640.9960.1541
2.91-3.660.11626620.9960.1191
3.66-34.310.09927930.9960.1021

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XSCALEVERSION Jun 30, 2023data scaling
PHASER2.8.3phasing
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.31 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 1321 4.99 %
Rwork0.2039 --
obs0.2052 26496 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 28 145 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.909
X-RAY DIFFRACTIONf_dihedral_angle_d12.576781
X-RAY DIFFRACTIONf_chiral_restr0.067292
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.36441430.32752768X-RAY DIFFRACTION99
1.77-1.850.30791450.26272757X-RAY DIFFRACTION100
1.85-1.950.25911440.24212740X-RAY DIFFRACTION99
1.95-2.070.26631490.22932769X-RAY DIFFRACTION100
2.07-2.230.261440.21592780X-RAY DIFFRACTION100
2.23-2.450.29071440.20822797X-RAY DIFFRACTION100
2.45-2.810.22831480.21462790X-RAY DIFFRACTION100
2.81-3.530.21281470.21082853X-RAY DIFFRACTION100
3.54-34.310.20341570.17962921X-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)
14.08871.0577-3.2145.1846-1.09073.0716-0.07180.0852-0.2103-0.2972-0.45730.42621.0748-0.70770.41570.6453-0.0728-0.12830.644-0.02770.544624.527910.141726.2078
25.07930.8309-0.64975.19670.80924.1802-0.0970.05540.12060.06380.08930.056-0.01590.0259-0.00050.1723-0.0005-0.03530.18980.03790.195933.678518.323542.1544
32.92121.03590.02567.133-2.30157.76840.14330.22560.1649-1.0074-0.00810.26660.1490.138-0.10680.51440.07740.01630.30930.02880.253234.550521.439915.4996
43.19731.4654-5.20427.4998-1.75798.5588-0.3605-0.5941-0.08920.50840.0947-0.35920.35110.40610.26850.31470.0071-0.03160.37420.06140.266936.131410.989149.3777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 249 through 268 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 219 )
4X-RAY DIFFRACTION4chain 'B' and (resid 238 through 248 )

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