[English] 日本語
![](img/lk-miru.gif)
- PDB-7t1k: Crystal structure of a superbinder Fes SH2 domain (sFes1) in comp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7t1k | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a superbinder Fes SH2 domain (sFes1) in complex with a high affinity phosphopeptide | ||||||||||||
![]() |
| ||||||||||||
![]() | SIGNALING PROTEIN / Src Homology 2 (SH2) / superbinder / engineered / phage display | ||||||||||||
Function / homology | ![]() terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / positive regulation of myeloid cell differentiation / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / positive regulation of myeloid cell differentiation / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / negative regulation of p38MAPK cascade / Netrin-1 signaling / cortical microtubule organization / uropod / regulation of mast cell degranulation / astral microtubule organization / postsynaptic actin cytoskeleton organization / positive regulation of protein localization to early endosome / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of multicellular organism growth / CRMPs in Sema3A signaling / filopodium assembly / protein-containing complex localization / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / establishment of endothelial barrier / sphingosine-1-phosphate receptor signaling pathway / Sensory processing of sound by outer hair cells of the cochlea / S100 protein binding / Sensory processing of sound by inner hair cells of the cochlea / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / protein kinase A binding / negative regulation of interleukin-2 production / microvillus membrane / negative regulation of T cell receptor signaling pathway / leukocyte cell-cell adhesion / cortical cytoskeleton / regulation of cell differentiation / protein kinase A regulatory subunit binding / Recycling pathway of L1 / plasma membrane raft / protein kinase A catalytic subunit binding / brush border / microvillus / actin filament bundle assembly / Sema3A PAK dependent Axon repulsion / immunological synapse / regulation of cell adhesion / cellular response to cAMP / positive regulation of microtubule polymerization / cell adhesion molecule binding / immunoglobulin receptor binding / ruffle / protein kinase A signaling / phosphatidylinositol binding / ciliary basal body / filopodium / cell projection / cell periphery / protein localization to plasma membrane / actin filament / positive regulation of protein localization to plasma membrane / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / receptor internalization / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / fibrillar center / ruffle membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of protein catabolic process / chemotaxis / microtubule cytoskeleton / disordered domain specific binding / actin filament binding / actin cytoskeleton / apical part of cell / actin binding / regulation of cell population proliferation / regulation of cell shape / ATPase binding / cytoplasmic vesicle / actin cytoskeleton organization / microtubule binding / basolateral plasma membrane / protein tyrosine kinase activity / vesicle / protein autophosphorylation / cell adhesion / endosome / cadherin binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Martyn, G.D. / Singer, A.U. / Veggiani, G. / Kurinov, I. / Sicheri, F. / Sidhu, S.S. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 102.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t1lC ![]() 7t1uC ![]() 3bkbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 11613.306 Da / Num. of mol.: 1 / Fragment: SH2 domain / Mutation: S485G, G487S, K488Q, Q489P, E490D Source method: isolated from a genetically manipulated source Details: Superbinder version of the Fes SH2 domain engineered using phage display Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P07332, non-specific protein-tyrosine kinase |
---|---|
#2: Protein/peptide | Mass: 879.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fragment of Ezrin protein / Source: (synth.) ![]() |
-Non-polymers , 5 types, 123 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-MLI / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.4 M Sodium Malonate (pH 5.5) and 2% PEG300 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2019 / 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: 1.25→58.89 Å / Num. obs: 40953 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 12.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 11.2 % / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2021 / CC1/2: 0.463 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3BKB Resolution: 1.25→57.23 Å / SU ML: 0.1194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.908 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→57.23 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|