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- PDB-6o8c: Crystal structure of STING CTT in complex with TBK1 -

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Basic information

Entry
Database: PDB / ID: 6o8c
TitleCrystal structure of STING CTT 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


Interleukin-37 signaling / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / TNFR1-induced proapoptotic signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Negative regulators of DDX58/IFIH1 signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PINK1-PRKN Mediated Mitophagy / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of TNFR1 signaling ...Interleukin-37 signaling / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / TNFR1-induced proapoptotic signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Negative regulators of DDX58/IFIH1 signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PINK1-PRKN Mediated Mitophagy / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of TNFR1 signaling / STING complex / STAT6-mediated induction of chemokines / positive regulation of xenophagy / Regulation of innate immune responses to cytosolic DNA / 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 / proton channel activity / cGAS/STING signaling pathway / regulation of metabolic process / reticulophagy / pattern recognition receptor signaling pathway / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / positive regulation of interferon-alpha production / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of type I interferon production / cellular response to interferon-beta / negative regulation of TORC1 signaling / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of TORC1 signaling / endoplasmic reticulum-Golgi intermediate compartment membrane / peptidyl-threonine phosphorylation / activation of innate immune response / cytoplasmic vesicle membrane / Regulation of innate immune responses to cytosolic DNA / autophagosome / positive regulation of interferon-beta production / positive regulation of DNA-binding transcription factor activity / secretory granule membrane / phosphoprotein binding / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / peptidyl-serine phosphorylation / regulation of gene expression / regulation of inflammatory response / protein phosphatase binding / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / nucleic acid binding / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of canonical NF-kappaB signal transduction / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / endosome / ciliary basal body / cilium / 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
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,3296
Polymers161,1464
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 area6910 Å2
ΔGint-28 kcal/mol
Surface area66100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.510, 249.510, 243.783
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 Serine/threonine-protein kinase TBK1 / T2K / TANK-binding kinase 1


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 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: 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 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: 6.8 Å3/Da / Density % sol: 81.9 %
Crystal growTemperature: 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

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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: 3.17→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 shellResolution: 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

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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: 4JLC

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
RfactorNum. reflection% reflection
Rfree0.2305 3720 4.9 %
Rwork0.2135 --
obs0.2143 75886 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.17→81.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10527 0 68 0 10595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210830
X-RAY DIFFRACTIONf_angle_d1.08614616
X-RAY DIFFRACTIONf_dihedral_angle_d17.4136529
X-RAY DIFFRACTIONf_chiral_restr0.0541610
X-RAY DIFFRACTIONf_plane_restr0.0051863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.21010.42671560.38442596X-RAY DIFFRACTION100
3.2101-3.25240.39681170.35022649X-RAY DIFFRACTION100
3.2524-3.29690.34391480.32982617X-RAY DIFFRACTION100
3.2969-3.3440.35021300.32392632X-RAY DIFFRACTION100
3.344-3.3940.33961510.29812626X-RAY DIFFRACTION100
3.394-3.4470.33061130.2892660X-RAY DIFFRACTION100
3.447-3.50350.33151500.28082618X-RAY DIFFRACTION100
3.5035-3.56390.30851310.27492660X-RAY DIFFRACTION100
3.5639-3.62870.31751460.27472638X-RAY DIFFRACTION100
3.6287-3.69850.28941220.26412642X-RAY DIFFRACTION100
3.6985-3.7740.23051460.2482636X-RAY DIFFRACTION100
3.774-3.85610.25991310.23382639X-RAY DIFFRACTION100
3.8561-3.94580.25531320.21452662X-RAY DIFFRACTION100
3.9458-4.04440.2321390.21842652X-RAY DIFFRACTION100
4.0444-4.15380.21651420.21142647X-RAY DIFFRACTION100
4.1538-4.2760.22071500.19782650X-RAY DIFFRACTION100
4.276-4.4140.22531390.19262664X-RAY DIFFRACTION100
4.414-4.57180.20451090.1932678X-RAY DIFFRACTION100
4.5718-4.75480.21571470.19712668X-RAY DIFFRACTION100
4.7548-4.97120.19041630.18712657X-RAY DIFFRACTION100
4.9712-5.23320.21341490.18512660X-RAY DIFFRACTION100
5.2332-5.5610.22171200.19842712X-RAY DIFFRACTION100
5.561-5.99030.22551140.22462740X-RAY DIFFRACTION100
5.9903-6.59290.24121400.22572723X-RAY DIFFRACTION100
6.5929-7.54630.24991460.20982725X-RAY DIFFRACTION100
7.5463-9.50520.15951500.15682774X-RAY DIFFRACTION100
9.5052-81.69840.16521390.16932941X-RAY DIFFRACTION99
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)
11.88781.9431-0.2447.2156-1.68962.9044-0.1361-0.3921-0.17610.3736-0.1279-0.1964-0.15030.15370.26280.87490.18390.07610.70040.00830.4344118.1298-52.49477.4187
21.5174-1.04930.71772.3678-1.46350.9523-0.7154-0.8341-0.01730.36190.0825-0.5917-0.44140.07880.51071.19570.2436-0.09960.99150.09190.6939133.3568-42.848217.4736
32.6136-0.7691-0.6654.3627-0.95993.0571-0.2707-0.51170.28080.70810.0862-0.2173-1.26580.12370.15521.35270.0297-0.14970.5379-0.13650.5141124.3313-21.09311.6682
42.1831-3.8733-0.30429.39650.38050.2350.0262-0.01160.3556-0.5752-0.0239-0.0434-0.2750.0054-0.00271.30260.0631-0.17410.5789-0.06850.7072117.2164-9.9157-21.4139
55.8512-2.1392-0.30512.02510.53230.9959-0.01760.4545-0.3069-0.6773-0.15650.0582-0.11190.00310.18941.33040.1115-0.08210.6361-0.09980.5118117.6257-55.211-42.6698
60.59920.37410.41382.92192.99163.1363-0.49560.28060.0623-0.46450.13430.5351-0.4503-0.12570.37991.35480.1481-0.24960.8147-0.15410.7575104.3694-57.0736-51.3541
72.10450.1333-0.88174.41291.44863.2784-0.06940.4155-0.0737-1.0037-0.26480.6354-0.7277-0.76730.28221.26890.297-0.50880.8133-0.10310.924992.1588-37.2448-40.8044
80.9564-1.08280.27475.7451-1.23991.6581-0.3307-0.13890.3090.30320.40620.6685-0.6158-0.4802-0.14791.07860.3436-0.270.7533-0.12391.05489.1391-17.9664-16.3848
92.7369-2.3650.55992.2365-1.41526.92160.58440.0707-0.2719-1.78120.12-1.47230.05771.702-0.96571.41740.16670.10020.9913-0.13910.9374140.7469-58.0658-31.8834
105.53872.279-4.32036.41310.12034.021.02763.0324-2.8498-0.0616-0.09741.09511.5967-0.6124-0.69491.4846-0.1738-0.30021.0422-0.23281.0335103.0702-71.9549-2.7147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 145 )
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 369 )
4X-RAY DIFFRACTION4chain 'A' and (resid 370 through 651 )
5X-RAY DIFFRACTION5chain 'B' and (resid -3 through 128 )
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 188 )
7X-RAY DIFFRACTION7chain 'B' and (resid 189 through 369 )
8X-RAY DIFFRACTION8chain 'B' and (resid 370 through 653 )
9X-RAY DIFFRACTION9chain 'D' and (resid 366 through 379 )
10X-RAY DIFFRACTION10chain 'E' and (resid 368 through 379 )

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