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- PDB-7ppn: SHP2 catalytic domain in complex with CD28 (183-198) phosphopepti... -

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Basic information

Entry
Database: PDB / ID: 7ppn
TitleSHP2 catalytic domain in complex with CD28 (183-198) phosphopeptide (pTyr-191, p-Thr-195)
Components
  • T-cell-specific surface glycoprotein CD28
  • Tyrosine-protein phosphatase non-receptor type 11,Tyrosine-protein phosphatase non-receptor type 11
KeywordsSIGNALING PROTEIN / SHP2 / Phosphatase / CD28 / phosphopeptide / signaling
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development ...Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / regulation of regulatory T cell differentiation / negative regulation of cell adhesion mediated by integrin / positive regulation of isotype switching to IgG isotypes / STAT5 Activation / Co-inhibition by BTLA / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / Netrin mediated repulsion signals / negative regulation of neutrophil activation / cerebellar cortex formation / positive regulation of hormone secretion / positive regulation of CD4-positive, alpha-beta T cell proliferation / 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 / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / CD28 dependent Vav1 pathway / 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 / peptide hormone receptor binding / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / positive regulation of interleukin-4 production / 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 / humoral immune response / phosphoprotein phosphatase activity / Regulation of IFNA/IFNB signaling / RET signaling / positive regulation of interleukin-10 production / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / immunological synapse / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / CD28 dependent PI3K/Akt signaling / 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 / positive regulation of viral genome replication / coreceptor activity / 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 / positive regulation of T cell proliferation / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 ...T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 / Immunoglobulin V-Type / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28 / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSok, P. / Zeke, A. / Remenyi, A.
Funding support Hungary, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)KKP 126963 Hungary
National Research Development and Innovation Office (NKFIH)PD120973 Hungary
Citation
Journal: Nat Commun / Year: 2022
Title: Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling.
Authors: Zeke, A. / Takacs, T. / Sok, P. / Nemeth, K. / Kirsch, K. / Egri, P. / Poti, A.L. / Bento, I. / Tusnady, G.E. / Remenyi, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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,Tyrosine-protein phosphatase non-receptor type 11
B: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9203
Polymers34,8282
Non-polymers921
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.190, 82.363, 147.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11,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: 32629.900 Da / Num. of mol.: 1 / Mutation: catalytic inactivation: C213S
Source method: isolated from a genetically manipulated source
Details: SHP2 catalytic domain was optimised for crystallisation and missing residues from 315 to 323 (original SHP2 sequence numbering), these missing residues in the optimised construct (74-77) ...Details: SHP2 catalytic domain was optimised for crystallisation and missing residues from 315 to 323 (original SHP2 sequence numbering), these missing residues in the optimised construct (74-77) were replaced to GSSG resideues.,SHP2 catalytic domain was optimised for crystallisation and missing residues from 315 to 323 (original SHP2 sequence numbering), these missing residues in the optimised construct (74-77) were replaced to GSSG resideues.
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide T-cell-specific surface glycoprotein CD28 / TP44


Mass: 2198.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphorylated residues: pTyr-191, p-Thr-195 / Source: (synth.) Homo sapiens (human) / References: UniProt: P10747
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.03 % / Description: rhomboid shaped crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG 20000, 100 mM Citrate buffer pH 5.5, 50 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N gas cryosteam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→49.25 Å / Num. obs: 26486 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 26.1 / Num. measured all: 341960
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.949.51.3441573716620.6460.4591.4231.899.5
9.11-49.2510.80.02307428510.0060.0218499.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.17refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZM0

3zm0


Resolution: 1.9→45.27 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 1998 7.56 %
Rwork0.1801 24442 -
obs0.1821 26440 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 6 50 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582405
X-RAY DIFFRACTIONf_angle_d0.87523258
X-RAY DIFFRACTIONf_chiral_restr0.0568345
X-RAY DIFFRACTIONf_plane_restr0.004426
X-RAY DIFFRACTIONf_dihedral_angle_d21.9672913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.33571390.28621709X-RAY DIFFRACTION99.3
1.95-20.28181400.23821690X-RAY DIFFRACTION99.62
2-2.060.25261420.20351754X-RAY DIFFRACTION100
2.06-2.130.24191390.20231704X-RAY DIFFRACTION100
2.13-2.20.21021410.17981714X-RAY DIFFRACTION99.78
2.2-2.290.2381430.18461748X-RAY DIFFRACTION99.95
2.29-2.390.24721410.18641727X-RAY DIFFRACTION99.84
2.39-2.520.23641420.19841742X-RAY DIFFRACTION99.79
2.52-2.680.24711430.20321735X-RAY DIFFRACTION99.89
2.68-2.880.21661420.21131748X-RAY DIFFRACTION99.84
2.88-3.170.23651430.20691755X-RAY DIFFRACTION100
3.18-3.630.20231450.18361759X-RAY DIFFRACTION99.84
3.63-4.580.18451470.15121801X-RAY DIFFRACTION99.85
4.58-45.270.16831510.1621856X-RAY DIFFRACTION99.8
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)
12.14371667208-2.59924348485-0.4630296015286.127521629480.9871444398575.154651032640.1767206468220.3723492968740.195067532804-0.388692255343-0.24745322945-0.8218775303090.09231064182710.5139664907660.07432433055240.282672821694-0.06691524944720.07121840710540.5308310018890.06391149175210.43279076922412.728980075220.7789331188-32.7526126857
21.57334934432-0.7248461059870.03362883795062.211835448550.4708490058463.46848448788-0.0421035616115-0.0690104343190.07383608583410.2888383752970.0126269992790.200807376518-0.11447771508-0.1640647957310.02967600622990.291243208657-0.001350190274460.04478514556430.321038410801-0.01643543385740.2971034768791.46905202125.4805818099-15.5261998251
32.33092305397-0.266672323211-0.4894874424823.876817665910.365703709263.14557998887-0.0575641444515-0.0895532573096-0.2959124004540.299640274506-0.001022441869870.3422976463940.524008925215-0.1514401503070.09018653766420.364170507165-0.02145211199670.0353851293010.3021132618990.002531657050170.3135425372023.973478684669.45631059428-17.4862654577
40.2683786487870.898736558503-0.2931428616453.01654406553-0.996993594760.3320284339930.5057861877161.624689157471.25148486334-1.358526481970.218646004922-0.599240585565-1.125076362620.983314683899-0.6049890853960.887528986018-0.1840828282410.0385401870810.7122653350720.04236812047191.0528948219119.43000570223.1760115705-22.0661663407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 4 through 35 )
2X-RAY DIFFRACTION2chain A and (resid 36 through 146 )
3X-RAY DIFFRACTION3chain A and (resid 147 through 282 )
4X-RAY DIFFRACTION4chain B and (resid 189 through 193 )

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