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- PDB-7m6t: Crystal structure of SOCS2/ElonginB/ElonginC bound to a non-canon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m6t | ||||||
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Title | Crystal structure of SOCS2/ElonginB/ElonginC bound to a non-canonical peptide that enhances phospho-peptide binding | ||||||
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![]() | SIGNALING PROTEIN / SH2 / E3 Ligase | ||||||
Function / homology | ![]() JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / growth hormone receptor signaling pathway ...JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / growth hormone receptor signaling pathway / Cul2-RING ubiquitin ligase complex / negative regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphatidylinositol phosphate biosynthetic process / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / mammary gland alveolus development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Growth hormone receptor signaling / cellular response to hormone stimulus / RNA Polymerase II Pre-transcription Events / Negative regulation of FLT3 / lactation / positive regulation of neuron differentiation / Interleukin-7 signaling / transcription corepressor binding / transcription elongation by RNA polymerase II / regulation of cell growth / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / insulin-like growth factor receptor binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / response to estradiol / protein-macromolecule adaptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / protein ubiquitination / intracellular signal transduction / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kershaw, N.J. / Li, K. / Linossi, E.M. / Nicholson, S.E. | ||||||
![]() | ![]() Title: Discovery of an exosite on the SOCS2-SH2 domain that enhances SH2 binding to phosphorylated ligands. Authors: Linossi, E.M. / Li, K. / Veggiani, G. / Tan, C. / Dehkhoda, F. / Hockings, C. / Calleja, D.J. / Keating, N. / Feltham, R. / Brooks, A.J. / Li, S.S. / Sidhu, S.S. / Babon, J.J. / Kershaw, N.J. / Nicholson, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.7 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.9 KB | Display | ![]() |
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Full document | ![]() | 472.7 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c9wS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 19342.121 Da / Num. of mol.: 1 / Mutation: K115A, K117A, Q118A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13251.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 10843.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 1476.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulphate Bis-Tris pH6.5 |
-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: Sep 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 3.194→43.383 Å / Num. obs: 8106 / % possible obs: 99.29 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3.194→3.308 Å / Num. unique obs: 780 / CC1/2: 0.782 / % possible all: 98.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2C9W Resolution: 3.194→43.383 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.93 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 218.73 Å2 / Biso mean: 110.4021 Å2 / Biso min: 75.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.194→43.383 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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