+Open data
-Basic information
Entry | Database: PDB / ID: 4jlc | ||||||
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Title | Crystal structure of mouse TBK1 bound to SU6668 | ||||||
Components | Serine/threonine-protein kinase TBK1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Interleukin-37 signaling / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TNFR1-induced proapoptotic signaling / Negative regulators of DDX58/IFIH1 signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy ...Interleukin-37 signaling / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TNFR1-induced proapoptotic signaling / Negative regulators of DDX58/IFIH1 signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy / Regulation of TNFR1 signaling / positive regulation of xenophagy / regulation of type I interferon production / dendritic cell proliferation / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of interferon-alpha production / activation of innate immune response / antiviral innate immune response / negative regulation of TORC1 signaling / positive regulation of interferon-beta production / positive regulation of TORC1 signaling / peptidyl-threonine phosphorylation / phosphoprotein binding / peptidyl-serine phosphorylation / regulation of gene expression / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / nucleic acid binding / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / protein phosphorylation / innate immune response / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Li, P. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural Insights into the Functions of TBK1 in Innate Antimicrobial Immunity. Authors: Shu, C. / Sankaran, B. / Chaton, C.T. / Herr, A.B. / Mishra, A. / Peng, J. / Li, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jlc.cif.gz | 278.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jlc.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jlc_validation.pdf.gz | 678.7 KB | Display | wwPDB validaton report |
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Full document | 4jlc_full_validation.pdf.gz | 690.1 KB | Display | |
Data in XML | 4jlc_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 4jlc_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/4jlc ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jlc | HTTPS FTP |
-Related structure data
Related structure data | 4jl9C 3qa8S 4eutS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 75690.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tbk1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9WUN2, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-SU6 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Sodium Citrate, 0.1 M HEPES, 10-14% isopropanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2013 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→70.53 Å / Num. all: 20027 / Num. obs: 20027 / % possible obs: 100 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 10.4 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3→3.18 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EUT AND 3QA8 Resolution: 3→70.53 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 29.89 / 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: 3→70.53 Å
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Refine LS restraints |
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LS refinement shell |
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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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