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Yorodumi- PDB-6roz: Structure of the N-SH2 domain of the human tyrosine-protein phosp... -
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-Basic information
Entry | Database: PDB / ID: 6roz | ||||||
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Title | Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based switch motif | ||||||
Components |
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Keywords | CELL CYCLE / Phosphatase / inhibitory peptide / signal transducer / Src homology-2 domains / ITSM / immune receptor tyrosine-based switch motif | ||||||
Function / homology | Function and homology information negative regulation of tolerance induction / regulatory T cell apoptotic process / 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 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / 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 / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / negative regulation of B cell apoptotic process / negative regulation of chondrocyte differentiation / Signaling by Leptin / 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 / triglyceride metabolic process / 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 / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / regulation of type I interferon-mediated signaling pathway / humoral immune response / 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 / PD-1 signaling / Regulation of IFNA/IFNB signaling / negative regulation of insulin secretion / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / regulation of immune response / 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 / homeostasis of number of cells within a tissue / FRS-mediated FGFR3 signaling / 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 / cell adhesion molecule binding / 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-phosphatase / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / Negative regulation of FGFR3 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Krausze, J. / Sikorska, J. / Carlomagno, T. | ||||||
Citation | Journal: Sci Adv / Year: 2020 Title: Molecular mechanism of SHP2 activation by PD-1 stimulation. Authors: Marasco, M. / Berteotti, A. / Weyershaeuser, J. / Thorausch, N. / Sikorska, J. / Krausze, J. / Brandt, H.J. / Kirkpatrick, J. / Rios, P. / Schamel, W.W. / Kohn, M. / Carlomagno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6roz.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6roz.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 6roz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/6roz ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6roz | HTTPS FTP |
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-Related structure data
Related structure data | 6r5gC 6royC 3tkzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 3 - 104 / Label seq-ID: 3 - 104
NCS ensembles : (Details: A, C) |
-Components
#1: Protein | Mass: 11790.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pEMT22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase #2: Protein/peptide | Mass: 1377.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized peptide / Source: (synth.) synthetic construct (others) / References: UniProt: Q15116*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 34.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 31.7% (w/v) PEG 3350, 0.1 M HEPES, 0.233 M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2016 / Details: TOROIDAL FOCUSING MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→53.28 Å / Num. obs: 4283 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 61.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.074 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.89→3.07 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 2 / Num. unique obs: 713 / CC1/2: 0.764 / Rpim(I) all: 0.552 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3tkz Resolution: 2.89→53.28 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.914 / SU B: 67.134 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.991 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→53.28 Å
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Refine LS restraints |
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