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- PDB-4iw0: Crystal structure and mechanism of activation of TBK1 -

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Basic information

Entry
Database: PDB / ID: 4iw0
TitleCrystal structure and mechanism of activation of TBK1
ComponentsSerine/threonine-protein kinase TBK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE / ATP binding / Phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / positive regulation of TORC2 signaling / dendritic cell proliferation / regulation of type I interferon production / T follicular helper cell differentiation / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN ...IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / positive regulation of TORC2 signaling / dendritic cell proliferation / regulation of type I interferon production / T follicular helper cell differentiation / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / Interleukin-37 signaling / cGAS/STING signaling pathway / 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 / positive regulation of interferon-alpha production / positive regulation of macroautophagy / peptidyl-threonine phosphorylation / 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 / TICAM1-dependent activation of IRF3/IRF7 / 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 autophagy / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / positive regulation of TORC1 signaling / activation of innate immune response / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interferon-beta production / Regulation of TNFR1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / phosphoprotein binding / macroautophagy / response to virus / SARS-CoV-1 activates/modulates innate immune responses / peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / protein phosphatase binding / defense response to virus / Potential therapeutics for SARS / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / protein phosphorylation / inflammatory response / negative regulation of gene expression / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
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 / : / 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 ...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 / : / 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 / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsLarabi, A. / Devos, J.M. / Ng, S.-L. / Nanao, M.H. / Round, A. / Maniatis, T. / Panne, D.
CitationJournal: Cell Rep / Year: 2013
Title: Crystal structure and mechanism of activation of TANK-binding kinase 1.
Authors: Larabi, A. / Devos, J.M. / Ng, S.L. / Nanao, M.H. / Round, A. / Maniatis, T. / Panne, D.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4372
Polymers75,8461
Non-polymers5911
Water00
1
A: Serine/threonine-protein kinase TBK1
hetero molecules

A: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,8744
Polymers151,6912
Non-polymers1,1832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3150 Å2
ΔGint-0 kcal/mol
Surface area62900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.910, 228.910, 97.980
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 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 75845.594 Da / Num. of mol.: 1 / Mutation: D135N
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
#2: 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.: 1 / Source method: obtained synthetically / Formula: C23H26IN7O2S
Has protein modificationY

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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: 4.89 Å3/Da / Density % sol: 74.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 13213 / Num. obs: 13213 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→47.559 Å / SU ML: 0.6 / σ(F): 1.99 / Phase error: 35.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2911 661 5 %RANDOM
Rwork0.2374 ---
obs0.2401 13213 99.71 %-
all-13213 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→47.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5253 0 34 0 5287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025400
X-RAY DIFFRACTIONf_angle_d0.5187292
X-RAY DIFFRACTIONf_dihedral_angle_d12.2632044
X-RAY DIFFRACTIONf_chiral_restr0.035802
X-RAY DIFFRACTIONf_plane_restr0.002930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.30880.37141280.3172443X-RAY DIFFRACTION99
4.3088-4.7420.31351290.26742454X-RAY DIFFRACTION100
4.742-5.42740.29251310.25592484X-RAY DIFFRACTION100
5.4274-6.83470.35991320.3012514X-RAY DIFFRACTION100
6.8347-47.56260.25331410.19632657X-RAY DIFFRACTION100

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