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- PDB-7emn: The atomic structure of SHP2 E76A mutant -

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Basic information

Entry
Database: PDB / ID: 7emn
TitleThe atomic structure of SHP2 E76A mutant
ComponentsTyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE / Phosphatase
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 / Netrin mediated repulsion signals / positive regulation of hormone secretion ...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 / Netrin mediated repulsion signals / positive regulation of hormone secretion / cerebellar cortex formation / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / negative regulation of chondrocyte differentiation / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / face morphogenesis / ERBB signaling pathway / Costimulation by the CD28 family / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / CTLA4 inhibitory signaling / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / PECAM1 interactions / phosphoprotein phosphatase activity / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / neurotrophin TRK receptor signaling pathway / inner ear development / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / Regulation of IFNA/IFNB signaling / PD-1 signaling / negative regulation of insulin secretion / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / GPVI-mediated activation cascade / cell adhesion molecule binding / cellular response to epidermal growth factor stimulus / Tie2 Signaling / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / Downstream signal transduction / axonogenesis / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein tyrosine kinase binding / protein-tyrosine-phosphatase / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / positive regulation of glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / brain development / insulin receptor binding / epidermal growth factor receptor signaling pathway
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 ...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 / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
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: 3 Å
AuthorsLuo, F. / Xie, J.J. / Zhu, J.D. / Liu, C.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A novel partially open state of SHP2 points to a "multiple gear" regulation mechanism.
Authors: Tao, Y. / Xie, J. / Zhong, Q. / Wang, Y. / Zhang, S. / Luo, F. / Wen, F. / Xie, J. / Zhao, J. / Sun, X. / Long, H. / Ma, J. / Zhang, Q. / Long, J. / Fang, X. / Lu, Y. / Li, D. / Li, M. / ...Authors: Tao, Y. / Xie, J. / Zhong, Q. / Wang, Y. / Zhang, S. / Luo, F. / Wen, F. / Xie, J. / Zhao, J. / Sun, X. / Long, H. / Ma, J. / Zhang, Q. / Long, J. / Fang, X. / Lu, Y. / Li, D. / Li, M. / Zhu, J. / Sun, B. / Li, G. / Diao, J. / Liu, C.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 5, 2021ID: 6IHZ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 11
B: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)122,7812
Polymers122,7812
Non-polymers00
Water57632
1
A: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)61,3901
Polymers61,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)61,3901
Polymers61,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.200, 211.450, 56.100
Angle α, β, γ (deg.)90.000, 96.960, 90.000
Int Tables number4
Space group name H-MP1211

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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: 61390.258 Da / Num. of mol.: 2 / Mutation: E76A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium formate, 0.1 M Bicine ph 8.5, 15% w/v PEG 5000MME

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→55.687 Å / Num. obs: 36697 / % possible obs: 99.7 % / Redundancy: 3.46 % / Biso Wilson estimate: 38.68 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.153 / Rrim(I) all: 0.181 / Χ2: 0.922 / Net I/σ(I): 5.82
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.522 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 2771 / CC1/2: 0.764 / Rrim(I) all: 0.796 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ATD

6atd


Resolution: 3→55.687 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 1061 5 %
Rwork0.2233 20174 -
obs0.2257 21235 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.26 Å2 / Biso mean: 39.9009 Å2 / Biso min: 12.66 Å2
Refinement stepCycle: final / Resolution: 3→55.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 0 32 7956
Biso mean---25.41 -
Num. residues----992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0001-3.13660.31631330.26652520100
3.1366-3.30190.33041340.26352549100
3.3019-3.50880.28441310.23942504100
3.5088-3.77960.30151320.23192506100
3.7796-4.15990.28221310.21622497100
4.1599-4.76160.23441320.1884251899
4.7616-5.99790.22441340.20482541100
Refinement TLS params.Method: refined / Origin x: 59.4962 Å / Origin y: 10.8204 Å / Origin z: 82.4897 Å
111213212223313233
T0.1504 Å2-0.0229 Å20.0283 Å2-0.1987 Å2-0.0356 Å2--0.1371 Å2
L0.3841 °2-0.2167 °20.0396 °2-0.742 °2-0.2352 °2--0.5294 °2
S-0.0216 Å °0.014 Å °0.007 Å °-0.091 Å °0.0404 Å °-0.0451 Å °0.0729 Å °-0.0053 Å °-0.0121 Å °
Refinement TLS groupSelection details: all

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