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- PDB-6o8b: Crystal structure of STING CTD in complex with TBK1 -

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Basic information

Entry
Database: PDB / ID: 6o8b
TitleCrystal structure of STING CTD in complex with TBK1
Components
  • Serine/threonine-protein kinase TBK1
  • Stimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Adaptor / Kinase / Complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / STING complex / STAT6-mediated induction of chemokines / positive regulation of xenophagy / protein localization to endoplasmic reticulum / positive regulation of TORC2 signaling / dendritic cell proliferation / 2',3'-cyclic GMP-AMP binding / regulation of type I interferon production / T follicular helper cell differentiation ...IRF3 mediated activation of type 1 IFN / STING complex / STAT6-mediated induction of chemokines / positive regulation of xenophagy / protein localization to endoplasmic reticulum / positive regulation of TORC2 signaling / dendritic cell proliferation / 2',3'-cyclic GMP-AMP binding / regulation of type I interferon production / T follicular helper cell differentiation / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / Interleukin-37 signaling / proton channel activity / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / reticulophagy / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / positive regulation of interferon-alpha production / autophagosome membrane / positive regulation of macroautophagy / peptidyl-threonine phosphorylation / autophagosome assembly / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / positive regulation of DNA-binding transcription factor activity / TICAM1-dependent activation of IRF3/IRF7 / cellular response to interferon-beta / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / negative regulation of TORC1 signaling / positive regulation of defense response to virus by host / signaling adaptor activity / positive regulation of autophagy / PINK1-PRKN Mediated Mitophagy / endoplasmic reticulum-Golgi intermediate compartment membrane / antiviral innate immune response / positive regulation of TORC1 signaling / activation of innate immune response / autophagosome / cytoplasmic vesicle membrane / protein serine/threonine kinase binding / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interferon-beta production / secretory granule membrane / Regulation of TNFR1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / phosphoprotein binding / macroautophagy / peptidyl-serine phosphorylation / response to virus / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / protein phosphatase binding / defense response to virus / DNA-binding transcription factor binding / mitochondrial outer membrane / Potential therapeutics for SARS / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein phosphorylation / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / endosome / defense response to Gram-positive bacterium / ciliary basal body / cilium / inflammatory response / Golgi membrane / negative regulation of gene expression / innate immune response / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Neutrophil degranulation / 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
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #420 / TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / : / : / STING transmembrane domain / : / : ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #420 / TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / : / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BX7 / Stimulator of interferon genes protein / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLi, P. / Zhao, B. / Du, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationA-1931-20170325 United States
CitationJournal: 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
DepositionMar 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Stimulator of interferon genes protein
E: Stimulator of interferon genes protein
A: Serine/threonine-protein kinase TBK1
B: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,4626
Polymers204,2794
Non-polymers1,1832
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-35 kcal/mol
Surface area61390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.690, 250.690, 239.241
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Stimulator of interferon genes protein / hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / ...hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / Transmembrane protein 173


Mass: 25675.973 Da / Num. of mol.: 2 / Mutation: T376E, F378M,S379W
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
#2: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 76463.344 Da / Num. of mol.: 2 / Mutation: D135N, S172E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBK1, NAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UHD2, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-BX7 / N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide


Mass: 591.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26IN7O2S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.32 Å3/Da / Density % sol: 76.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.8 M (NH4)2SO4, 0.1 M BIS-TRIS pH 5.5 and 1% PEG3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→82.058 Å / Num. obs: 60675 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.063 / Net I/σ(I): 7.8
Reflection shellResolution: 3.4→3.49 Å / Rmerge(I) obs: 2 / Num. unique obs: 4434 / Rpim(I) all: 0.86 / % possible all: 5.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IM2

4im2


Resolution: 3.4→82.058 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.88
RfactorNum. reflection% reflection
Rfree0.2578 3022 5.02 %
Rwork0.2435 --
obs0.2442 60195 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→82.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10829 0 68 0 10897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211131
X-RAY DIFFRACTIONf_angle_d0.57715029
X-RAY DIFFRACTIONf_dihedral_angle_d18.4456720
X-RAY DIFFRACTIONf_chiral_restr0.041651
X-RAY DIFFRACTIONf_plane_restr0.0031919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.45310.38751130.37472546X-RAY DIFFRACTION98
3.4531-3.50970.35761270.34662601X-RAY DIFFRACTION99
3.5097-3.57030.38551320.33862595X-RAY DIFFRACTION100
3.5703-3.63520.35921200.34522614X-RAY DIFFRACTION100
3.6352-3.70510.31911540.3322581X-RAY DIFFRACTION100
3.7051-3.78070.37631590.33212570X-RAY DIFFRACTION100
3.7807-3.86290.32221390.31082594X-RAY DIFFRACTION100
3.8629-3.95280.27931380.29962556X-RAY DIFFRACTION99
3.9528-4.05170.25951190.28952608X-RAY DIFFRACTION98
4.0517-4.16120.29571400.27512558X-RAY DIFFRACTION98
4.1612-4.28360.27361360.26082570X-RAY DIFFRACTION98
4.2836-4.42190.27171430.24952540X-RAY DIFFRACTION97
4.4219-4.57990.25841490.2412578X-RAY DIFFRACTION98
4.5799-4.76330.23671470.24472561X-RAY DIFFRACTION98
4.7633-4.980.22481510.22092548X-RAY DIFFRACTION98
4.98-5.24250.22231390.23042609X-RAY DIFFRACTION98
5.2425-5.57090.24551440.24262605X-RAY DIFFRACTION98
5.5709-6.0010.26291320.25372618X-RAY DIFFRACTION99
6.001-6.60460.23741420.25742608X-RAY DIFFRACTION97
6.6046-7.55970.25631460.24552643X-RAY DIFFRACTION98
7.5597-9.52220.19671290.17932660X-RAY DIFFRACTION97
9.5222-82.08140.22561230.17932810X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.03414.58680.34283.53640.27936.2204-0.59710.13560.1482-0.59450.42431.37810.1027-0.66970.64942.38750.3914-0.61011.83280.04692.1617-138.615361.0654-31.7953
27.4471.82180.43881.1378-2.11948.6058-0.30890.16180.70250.91030.7271-0.38320.0355-0.1474-0.25991.5329-0.224-0.1090.9439-0.1621.7572-103.188571.3266-2.595
35.64242.17930.2349.86421.90135.3238-0.11450.03450.6898-0.0992-0.1130.3982-0.9032-0.47860.3911.04750.0835-0.05230.7208-0.03720.7367-116.196664.53393.0108
41.49231.68760.55565.12350.23093.16520.0607-0.28370.12861.0323-0.45320.09970.3577-0.4320.33031.19330.05410.08380.7724-0.08890.6695-118.534749.23688.6622
53.62921.59581.33035.325-0.994.4226-0.5586-1.7736-0.2491.0942-0.19311.10830.0262-1.28450.73451.45430.01260.40631.2533-0.25491.0952-131.967740.427910.0344
61.2718-0.9464-0.03155.12810.9550.59120.15060.0146-0.33270.1085-0.2218-0.01360.6114-0.10760.08291.6082-0.02760.1870.59160.02960.8612-118.43611.8767-14.5929
75.1805-2.12390.26744.1175-0.08930.96680.2350.70240.4094-1.0617-0.36830.24950.20530.04090.16571.50970.18470.21450.84620.13690.831-115.266954.418-42.5801
83.15290.44130.66394.7011-1.31053.5040.08440.74140.5188-1.4331-0.2028-0.41140.38360.80750.07321.73940.37130.51221.04740.07611.1079-92.870738.9937-40.7304
91.044-1.5076-0.08035.38731.22961.2560.08070.0618-0.2344-0.05050.042-0.72910.54630.497-0.05841.48980.33830.21540.91050.10031.3231-88.987917.2599-15.7028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 369 through 379 )
2X-RAY DIFFRACTION2chain 'E' and (resid 368 through 379 )
3X-RAY DIFFRACTION3chain 'A' and (resid -5 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 246 )
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 656 )
7X-RAY DIFFRACTION7chain 'B' and (resid -2 through 165 )
8X-RAY DIFFRACTION8chain 'B' and (resid 166 through 378 )
9X-RAY DIFFRACTION9chain 'B' and (resid 379 through 654 )

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