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- PDB-5df6: Crystal structure of PTPN11 tandem SH2 domains in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 5df6
TitleCrystal structure of PTPN11 tandem SH2 domains in complex with a TXNIP peptide
Components
  • Tyrosine-protein phosphatase non-receptor type 11
  • txnip
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / negative regulation of cell division / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin ...cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / negative regulation of cell division / 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 / enzyme inhibitor activity / negative regulation of chondrocyte differentiation / triglyceride metabolic process / Signaling by Leptin / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / face morphogenesis / ERBB signaling pathway / Regulation of FOXO transcriptional activity by acetylation / Costimulation by the CD28 family / Signal regulatory protein family interactions / peptide hormone receptor binding / platelet formation / negative regulation of type I interferon production / megakaryocyte development / organ growth / 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 / inner ear development / phosphoprotein phosphatase activity / MAPK1 (ERK2) activation / PECAM1 interactions / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / Bergmann glial cell differentiation / regulation of type I interferon-mediated signaling pathway / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / regulation of protein-containing complex assembly / RET signaling / peptidyl-tyrosine dephosphorylation / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / PD-1 signaling / Regulation of IFNA/IFNB signaling / negative regulation of insulin secretion / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / response to glucose / Purinergic signaling in leishmaniasis infection / response to mechanical stimulus / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / homeostasis of number of cells within a tissue / FRS-mediated FGFR3 signaling / keratinocyte differentiation / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / cellular response to epidermal growth factor stimulus / FRS-mediated FGFR1 signaling / Tie2 Signaling / GPVI-mediated activation cascade / protein tyrosine kinase binding / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / cell adhesion molecule binding / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / axonogenesis / Downstream signal transduction / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein dephosphorylation / protein-tyrosine-phosphatase / response to progesterone / DNA damage checkpoint signaling
Similarity search - Function
Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Arrestin-like, C-terminal / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase, catalytic domain ...Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Arrestin-like, C-terminal / SH2 domain / SHC Adaptor Protein / 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 / Immunoglobulin E-set / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11 / Thioredoxin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.78 Å
AuthorsDong, A. / Li, W. / Tempel, W. / Liu, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2016
Title: Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP.
Authors: Liu, Y. / Lau, J. / Li, W. / Tempel, W. / Li, L. / Dong, A. / Narula, A. / Qin, S. / Min, J.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionSep 23, 2015ID: 5c96
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Data collection
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Dec 21, 2016Group: Non-polymer description
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: txnip
C: txnip


Theoretical massNumber of molelcules
Total (without water)31,75710
Polymers31,7573
Non-polymers07
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-21 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.470, 72.166, 62.547
Angle α, β, γ (deg.)90.00, 101.77, 90.00
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 / Shp2 / SH-PTP3


Mass: 28750.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pET28-SacB-AP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide txnip


Mass: 1503.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.78→46.69 Å / Num. obs: 23333 / % possible obs: 98.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.2
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.4 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
Aimless0.5.14data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
ARPmodel building
HKL-3000data processing
RefinementStarting model: 3TKZ AND 4XZ0

3tkz

4xz0


Resolution: 1.78→46.69 Å / SU B: 3.725 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.133
Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. PHENIX.MOLPROBITY WAS USED FOR GEOMETRY VALIDATION. JLIGAND AND THE GRADE SERVER WERE USED IN RESTRAINT PREPARATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1156 5 %RANDOM
Rwork0.194 ---
obs0.196 22177 98.4 %-
Displacement parametersBiso mean: 30.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.42 Å2
2--3.05 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 1.78→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 9 110 1891

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