+Open data
-Basic information
Entry | Database: PDB / ID: 6o8c | ||||||
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Title | Crystal structure of STING CTT in complex with TBK1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Adaptor / kinase / 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 / STING complex / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / positive regulation of xenophagy / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / regulation of type I interferon production / dendritic cell proliferation / proton channel activity / 2',3'-cyclic GMP-AMP binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / reticulophagy / cellular response to exogenous dsRNA / toll-like receptor 4 signaling pathway / positive regulation of interferon-alpha production / cellular response to organic cyclic compound / positive regulation of type I interferon production / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / activation of innate immune response / antiviral innate immune response / negative regulation of TORC1 signaling / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / positive regulation of TORC1 signaling / autophagosome / protein complex oligomerization / Regulation of innate immune responses to cytosolic DNA / secretory granule membrane / peptidyl-threonine phosphorylation / positive regulation of DNA-binding transcription factor activity / phosphoprotein binding / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / regulation of inflammatory response / peptidyl-serine phosphorylation / regulation of gene expression / protein phosphatase binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / nucleic acid binding / non-specific serine/threonine protein kinase / endosome / defense response to Gram-positive bacterium / protein phosphorylation / Golgi membrane / innate immune response / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å | ||||||
Authors | Li, P. / Zhao, B. / Du, F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2019 Title: A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1. Authors: Zhao, B. / Du, F. / Xu, P. / Shu, C. / Sankaran, B. / Bell, S.L. / Liu, M. / Lei, Y. / Gao, X. / Fu, X. / Zhu, F. / Liu, Y. / Laganowsky, A. / Zheng, X. / Ji, J.Y. / West, A.P. / Watson, R.O. / Li, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o8c.cif.gz | 542.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o8c.ent.gz | 455.2 KB | Display | PDB format |
PDBx/mmJSON format | 6o8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o8c_validation.pdf.gz | 369.5 KB | Display | wwPDB validaton report |
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Full document | 6o8c_full_validation.pdf.gz | 376.4 KB | Display | |
Data in XML | 6o8c_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 6o8c_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/6o8c ftp://data.pdbj.org/pub/pdb/validation_reports/o8/6o8c | HTTPS FTP |
-Related structure data
Related structure data | 6o8bC 4jlcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 76359.070 Da / Num. of mol.: 2 / Mutation: S172A 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 #2: Protein/peptide | Mass: 4213.761 Da / Num. of mol.: 2 / Mutation: V343W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q86WV6 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.8 Å3/Da / Density % sol: 81.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18% v/v tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 2% PEG3350 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2017 |
Radiation | Monochromator: Double-crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.17→81.671 Å / Num. obs: 76001 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.054 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 3.17→3.24 Å / Redundancy: 11.3 % / Rmerge(I) obs: 2.7 / Num. unique obs: 4418 / Rpim(I) all: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JLC Resolution: 3.17→81.671 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.17→81.671 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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