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- PDB-5x94: Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex -

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Basic information

Entry
Database: PDB / ID: 5x94
TitleCrystal structure of SHP2_SH2-CagA EPIYA_D peptide complex
Components
  • Cag pathogenicity island protein
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE / Helicobacter pylori CagA / SH2 domain-containing protein tyrosine phosphatase 2 (SHP2) / CagA polymorphism
Function / homology
Function and homology information


toxin transmembrane transporter activity / 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 ...toxin transmembrane transporter activity / 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 / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / 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 / Regulation of IFNA/IFNB signaling / PI3K Cascade / PD-1 signaling / 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 / negative regulation of insulin secretion / 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 / Tie2 Signaling / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / GPVI-mediated activation cascade / 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 / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine kinase binding / 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 / insulin receptor binding / epidermal growth factor receptor signaling pathway
Similarity search - Function
Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. ...Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cag pathogenicity island protein / Cytotoxicity-associated immunodominant antigen / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSenda, M. / Senda, T.
CitationJournal: Cell Rep / Year: 2017
Title: Differential Mechanisms for SHP2 Binding and Activation Are Exploited by Geographically Distinct Helicobacter pylori CagA Oncoproteins.
Authors: Hayashi, T. / Senda, M. / Suzuki, N. / Nishikawa, H. / Ben, C. / Tang, C. / Nagase, L. / Inoue, K. / Senda, T. / Hatakeyama, M.
History
DepositionMar 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
L: Cag pathogenicity island protein
M: Cag pathogenicity island protein
N: Cag pathogenicity island protein
O: Cag pathogenicity island protein


Theoretical massNumber of molelcules
Total (without water)56,0876
Polymers56,0876
Non-polymers00
Water39622
1
A: Tyrosine-protein phosphatase non-receptor type 11
L: Cag pathogenicity island protein
N: Cag pathogenicity island protein


Theoretical massNumber of molelcules
Total (without water)28,0443
Polymers28,0443
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-27 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 11
M: Cag pathogenicity island protein
O: Cag pathogenicity island protein


Theoretical massNumber of molelcules
Total (without water)28,0443
Polymers28,0443
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-22 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.184, 121.968, 72.171
Angle α, β, γ (deg.)90.00, 101.26, 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: 25006.480 Da / Num. of mol.: 2 / Fragment: SH2 domain (UNP RESIDUES 1-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide
Cag pathogenicity island protein


Mass: 1518.514 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 950-962 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori (bacteria) / References: UniProt: E6NP29, UniProt: P55980*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 31% PEG 4000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→70.8 Å / Num. obs: 28721 / % possible obs: 98.9 % / Redundancy: 3.7 % / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DGP

4dgp


Resolution: 2.6→70.781 Å / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 32.86
RfactorNum. reflection% reflection
Rfree0.2459 1459 5.09 %
Rwork0.1569 --
obs0.1632 28677 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→70.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 0 22 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083602
X-RAY DIFFRACTIONf_angle_d1.0514888
X-RAY DIFFRACTIONf_dihedral_angle_d16.9992097
X-RAY DIFFRACTIONf_chiral_restr0.052537
X-RAY DIFFRACTIONf_plane_restr0.006631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6048-2.69780.32471300.18792486X-RAY DIFFRACTION87
2.6978-2.80560.33331420.19572755X-RAY DIFFRACTION95
2.8056-2.93310.2871500.19022710X-RAY DIFFRACTION95
2.9331-3.08740.291450.17362745X-RAY DIFFRACTION95
3.0874-3.28030.26571520.1672745X-RAY DIFFRACTION95
3.2803-3.53280.28551430.15352765X-RAY DIFFRACTION95
3.5328-3.88680.2331490.14842683X-RAY DIFFRACTION95
3.8868-4.44570.21951480.12982723X-RAY DIFFRACTION95
4.4457-5.58790.15571540.12692766X-RAY DIFFRACTION95
5.5879-23.06330.19361370.16672713X-RAY DIFFRACTION95

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