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- PDB-6c7y: Crystal structure of inhibitory protein SOCS1 in complex with JAK... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c7y | ||||||||||||
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Title | Crystal structure of inhibitory protein SOCS1 in complex with JAK1 kinase domain | ||||||||||||
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![]() | SIGNALING PROTEIN / TRANSFERASE/INHIBITOR / Kinase / Kinase Inhibitor / TRANSFERASE-INHIBITOR complex | ||||||||||||
Function / homology | ![]() : / Interferon gamma signaling / Regulation of IFNG signaling / Interferon alpha/beta signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of CD8-positive, alpha-beta T cell differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / protein localization to cell-cell junction ...: / Interferon gamma signaling / Regulation of IFNG signaling / Interferon alpha/beta signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of CD8-positive, alpha-beta T cell differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / protein localization to cell-cell junction / kinase inhibitor activity / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-10-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / 1-phosphatidylinositol-3-kinase regulator activity / interleukin-15-mediated signaling pathway / positive regulation of regulatory T cell differentiation / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / phosphatidylinositol 3-kinase complex / regulation of growth / Interleukin-2 signaling / growth hormone receptor binding / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / type I interferon-mediated signaling pathway / Interleukin-6 signaling / fat cell differentiation / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / Interleukin-10 signaling / extrinsic component of cytoplasmic side of plasma membrane / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / phosphatidylinositol phosphate biosynthetic process / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / negative regulation of insulin receptor signaling pathway / regulation of cytokine production / insulin-like growth factor receptor binding / Interleukin-7 signaling / cellular response to amino acid stimulus / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / cytoplasmic side of plasma membrane / cellular response to virus / ISG15 antiviral mechanism / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / cytoplasmic ribonucleoprotein granule / Interferon gamma signaling / Interferon alpha/beta signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / endosome / protein ubiquitination / protein phosphorylation / response to antibiotic / focal adhesion / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Liau, N.P.D. / Laktyushin, A. / Lucet, I.S. / Murphy, J.M. / Yao, S. / Callaghan, K. / Nicola, N.A. / Kershaw, N.J. / Babon, J.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The molecular basis of JAK/STAT inhibition by SOCS1. Authors: Liau, N.P.D. / Laktyushin, A. / Lucet, I.S. / Murphy, J.M. / Yao, S. / Whitlock, E. / Callaghan, K. / Nicola, N.A. / Kershaw, N.J. / Babon, J.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179 KB | Display | ![]() |
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PDB format | ![]() | 139.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6c5xSC ![]() 3eyhS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32938.691 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 869-1153) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P23458, non-specific protein-tyrosine kinase |
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#2: Protein | Mass: 13162.991 Da / Num. of mol.: 1 / Fragment: UNP residues 48-164 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 42 molecules ![](data/chem/img/ADP.gif)
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![](data/chem/img/HOH.gif)
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#3: Chemical | ChemComp-ADP / | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM HEPES pH 7.0, 14% (w/v) PEG8000, 100mM magnesium acetate, 2mM TCEP |
-Data collection
Diffraction | Mean temperature: 77 K / Ambient temp details: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→40.613 Å / Num. obs: 20768 / % possible obs: 99.9 % / Redundancy: 8.268 % / Biso Wilson estimate: 54.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.121 / Χ2: 1.025 / Net I/σ(I): 15.77 / Num. measured all: 171700 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 6C5X & 3EYH Resolution: 2.499→40.613 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.35 / 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: 203.28 Å2 / Biso mean: 86.2543 Å2 / Biso min: 25.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.499→40.613 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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