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- PDB-7t1u: Crystal structure of a superbinder Src SH2 domain (sSrcF) in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t1u | ||||||||||||
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Title | Crystal structure of a superbinder Src SH2 domain (sSrcF) in complex with a high affinity phosphopeptide | ||||||||||||
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![]() | SIGNALING PROTEIN / Src Homology 2 (SH2) / rationally engineered / phosphotyrosine | ||||||||||||
Function / homology | ![]() regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / response to mineralocorticoid / positive regulation of dephosphorylation / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / entry of bacterium into host cell / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / Activated NTRK2 signals through FYN / positive regulation of integrin activation / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / : / intestinal epithelial cell development / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / response to acidic pH / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / podosome / regulation of bone resorption / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / myoblast proliferation / EPH-Ephrin signaling / odontogenesis / negative regulation of mitochondrial depolarization / Ephrin signaling / cellular response to peptide hormone stimulus / osteoclast development / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / Receptor Mediated Mitophagy / CTLA4 inhibitory signaling / GP1b-IX-V activation signalling / oogenesis / interleukin-6-mediated signaling pathway / leukocyte migration / phospholipase activator activity / DNA biosynthetic process / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of hippo signaling / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / positive regulation of Notch signaling pathway / Signaling by EGFR / cellular response to platelet-derived growth factor stimulus / stress fiber assembly / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / progesterone receptor signaling pathway / RUNX2 regulates osteoblast differentiation / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / uterus development / phospholipase binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Long-term potentiation / neurotrophin TRK receptor signaling pathway / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of telomere maintenance via telomerase / negative regulation of anoikis / RET signaling / FCGR activation Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Martyn, G.D. / Singer, A.U. / Manczyk, N. / Veggiani, G. / Kurinov, I. / Sicheri, F. / Sidhu, S.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Engineered SH2 Domains for Targeted Phosphoproteomics. Authors: Martyn, G.D. / Veggiani, G. / Kusebauch, U. / Morrone, S.R. / Yates, B.P. / Singer, A.U. / Tong, J. / Manczyk, N. / Gish, G. / Sun, Z. / Kurinov, I. / Sicheri, F. / Moran, M.F. / Moritz, R.L. / Sidhu, S.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 | ![]() | 113.4 KB | Display | ![]() |
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PDB format | ![]() | 81.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 455.5 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t1kC ![]() 7t1lC ![]() 4f5aS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 12659.173 Da / Num. of mol.: 2 / Fragment: SH2 domain Mutation: Residues 180 to 188 mutated from SETTKGAYC to GQSQPDYV and K206I (numbered as residue 205 in these coordinates) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P12931, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 986.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 80 uM Zinc Acetate, 12% PEG3350, 100 mM Sodium Acetate (pH 4.0), and 2% 1,3-butanediol Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2018 / Details: mirrors |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→51.57 Å / Num. obs: 5824 / % possible obs: 86.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 53.32 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 729 / CC1/2: 0.919 / % possible all: 88.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4F5A Resolution: 2.65→51.57 Å / SU ML: 0.4392 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.2581 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.06 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→51.57 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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