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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 / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / cellular response to oxidised low-density lipoprotein particle stimulus / genitalia development / atrioventricular canal development / negative regulation of cell division / negative regulation of cell adhesion mediated by integrin ...cellular response to tumor cell / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / cellular response to oxidised low-density lipoprotein particle stimulus / genitalia development / atrioventricular canal development / negative regulation of cell division / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / positive regulation of hormone secretion / regulation of protein export from nucleus / positive regulation of ossification / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / Signaling by Leptin / hormone metabolic process / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / Regulation of FOXO transcriptional activity by acetylation / 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 / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / RET signaling / Regulation of IFNA/IFNB signaling / The NLRP3 inflammasome / non-membrane spanning protein tyrosine phosphatase activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / enzyme inhibitor activity / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / positive regulation of insulin receptor signaling pathway / response to mechanical stimulus / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / response to glucose / Activated NTRK2 signals through FRS2 and FRS3 / Regulation of IFNG signaling / Purinergic signaling in leishmaniasis infection / keratinocyte differentiation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / Signaling by FLT3 ITD and TKD mutants / negative regulation of T cell proliferation / T cell costimulation / hormone-mediated signaling pathway / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / cell adhesion molecule binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / FLT3 Signaling / protein-tyrosine-phosphatase / homeostasis of number of cells within a tissue / Downstream signal transduction / axonogenesis / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / response to progesterone / positive regulation of interferon-beta production / protein tyrosine kinase binding
Similarity search - Function
: / Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 / Arrestin-like, C-terminal / SH2 domain / SHC Adaptor Protein ...: / Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 / 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
Revision 1.8Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 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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