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- PDB-4jmh: Crystal structure of synthetic protein in complex with double pY ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jmh | ||||||
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Title | Crystal structure of synthetic protein in complex with double pY peptide | ||||||
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![]() | DE NOVO PROTEIN / Synthetic protein / binding to double pY containing sequence | ||||||
Function / homology | ![]() regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Interleukin-2 signaling / Shc-EGFR complex / epidermal growth factor binding / epidermal growth factor receptor binding ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Interleukin-2 signaling / Shc-EGFR complex / epidermal growth factor binding / epidermal growth factor receptor binding / Signaling by ALK / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / Tie2 Signaling / SHC1 events in EGFR signaling / ephrin receptor binding / phosphotyrosine residue binding / SHC1 events in ERBB2 signaling / Integrin signaling / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / negative regulation of angiogenesis / insulin-like growth factor receptor signaling pathway / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / insulin-like growth factor receptor binding / Constitutive Signaling by EGFRvIII / insulin receptor binding / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / phospholipid binding / receptor tyrosine kinase binding / cellular response to growth factor stimulus / cell-cell adhesion / GPER1 signaling / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by ALK fusions and activated point mutants / insulin receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / heart development / actin cytoskeleton organization / RAF/MAP kinase cascade / angiogenesis / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / mitochondrial matrix / defense response to bacterium / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | synthetic construct (others)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yasui, N. / Smith, L. / Koide, S. | ||||||
![]() | ![]() Title: Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. Authors: Yasui, N. / Findlay, G.M. / Gish, G.D. / Hsiung, M.S. / Huang, J. / Tucholska, M. / Taylor, L. / Smith, L. / Boldridge, W.C. / Koide, A. / Pawson, T. / Koide, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.3 KB | Display | ![]() |
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PDB format | ![]() | 38.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jmgSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22333.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 1739.625 Da / Num. of mol.: 1 / Fragment: unp residues 344-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.66% ammonium sulfate, 2.32% PEG400, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03316 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 9059 / Num. obs: 9059 / % possible obs: 100 % / Observed criterion σ(I): -3 / Net I/σ(I): 21.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JMG Resolution: 2.408→32.173 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 29.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.408→32.173 Å
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Refine LS restraints |
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LS refinement shell |
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