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- PDB-4im0: Structure of Tank-Binding Kinase 1 -

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Basic information

Entry
Database: PDB / ID: 4im0
TitleStructure of Tank-Binding Kinase 1
ComponentsSerine/threonine-protein kinase TBK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / serine/threonine kinase / MRT67307 / 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 / serine/threonine protein kinase complex / regulation of type I interferon production / dendritic cell proliferation / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / Interleukin-37 signaling / TNFR1-induced proapoptotic signaling ...IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / serine/threonine protein kinase complex / regulation of type I interferon production / dendritic cell proliferation / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / Interleukin-37 signaling / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / positive regulation of macroautophagy / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / positive regulation of autophagy / negative regulation of TORC1 signaling / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of TORC1 signaling / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / activation of innate immune response / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / phosphoprotein binding / peptidyl-threonine phosphorylation / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / defense response to virus / protein phosphatase binding / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / nucleic acid binding / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / inflammatory response / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / innate immune response / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / 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) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-1FV / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4001 Å
AuthorsTu, D. / Eck, M.J.
CitationJournal: Cell Rep / Year: 2013
Title: Structure and ubiquitination-dependent activation of TANK-binding kinase 1.
Authors: Tu, D. / Zhu, Z. / Zhou, A.Y. / Yun, C.H. / Lee, K.E. / Toms, A.V. / Li, Y. / Dunn, G.P. / Chan, E. / Thai, T. / Yang, S. / Ficarro, S.B. / Marto, J.A. / Jeon, H. / Hahn, W.C. / Barbie, D.A. / Eck, M.J.
History
DepositionJan 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)76,6502
Polymers76,1851
Non-polymers4651
Water5,260292
1
A: Serine/threonine-protein kinase TBK1
hetero molecules

A: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2994
Polymers152,3702
Non-polymers9292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area3080 Å2
ΔGint-2 kcal/mol
Surface area61560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.921, 133.921, 85.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-852-

HOH

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Components

#1: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 76185.062 Da / Num. of mol.: 1 / Fragment: residues 1 to 657 / 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-1FV / N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide / MRT67307


Mass: 464.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36N6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 4% (w/v) PEG8000, 100 mM Tris pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: MD2 micro-diffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 35090 / Num. obs: 34873 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.55199.6
2.55-2.75199.6
2.75-3.02199.3
3.02-3.461100
3.46-4.361100
4.36-50197.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4001→39.024 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1748 5.04 %random
Rwork0.1993 ---
all0.2012 34940 --
obs0.2012 34682 99.26 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.922 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0634 Å20 Å20 Å2
2---4.0634 Å20 Å2
3---8.1267 Å2
Refinement stepCycle: LAST / Resolution: 2.4001→39.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 34 292 5257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055088
X-RAY DIFFRACTIONf_angle_d0.8896879
X-RAY DIFFRACTIONf_dihedral_angle_d15.6211895
X-RAY DIFFRACTIONf_chiral_restr0.055768
X-RAY DIFFRACTIONf_plane_restr0.003877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.47070.34141220.27212733X-RAY DIFFRACTION100
2.4707-2.55040.27051500.25852742X-RAY DIFFRACTION100
2.5504-2.64160.32291480.26012702X-RAY DIFFRACTION100
2.6416-2.74730.36751390.26242757X-RAY DIFFRACTION100
2.7473-2.87230.35831470.26042696X-RAY DIFFRACTION99
2.8723-3.02370.35261500.24632724X-RAY DIFFRACTION99
3.0237-3.21310.30381550.2412716X-RAY DIFFRACTION100
3.2131-3.4610.25671470.22292766X-RAY DIFFRACTION100
3.461-3.8090.2081530.19472756X-RAY DIFFRACTION100
3.809-4.35960.20471420.16922768X-RAY DIFFRACTION100
4.3596-5.49020.22011520.16862788X-RAY DIFFRACTION99
5.4902-39.02910.18981430.18682786X-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)
14.3907-1.0355-1.10473.12491.692.56440.03370.3216-1.3509-0.5632-0.12870.10940.6389-0.01390.04940.80150.06040.04770.402-0.01050.7962103.551216.0611-31.7997
26.44822.7475-0.68485.871-3.5569.0619-0.3051-0.7618-1.4526-0.16640.25860.91341.5749-0.4627-0.00310.64630.00130.1640.5830.14331.002584.028515.8643-12.2129
32.7522-0.0020.04633.88871.00251.5366-0.0391-0.06350.0371-0.2459-0.0160.6124-0.2242-0.37560.03160.36950.06690.02950.43310.06150.445588.806745.022-14.6174
48.9259-7.2085-0.4715.37090.3175-0.0747-1.1766-0.41650.67521.84720.6321-0.1345-0.645-0.70360.67271.2250.5266-0.29461.1408-0.33810.969273.347289.1813-1.8101
54.6946-0.61020.88814.4069-0.58842.2223-0.1348-0.5003-0.62670.38650.2621-0.8870.44810.11340.05650.37310.0860.09590.40210.27520.2964108.163129.52430.6272
63.7141-4.44093.44074.1857-3.19521.6077-0.7404-1.09070.52410.33520.59160.389-0.4506-0.27080.00440.80170.30350.03930.7537-0.03690.894778.674570.2234-5.0842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:216)
2X-RAY DIFFRACTION2chain 'A' and (resseq 217:270)
3X-RAY DIFFRACTION3chain 'A' and (resseq 271:470)
4X-RAY DIFFRACTION4chain 'A' and (resseq 471:526)
5X-RAY DIFFRACTION5chain 'A' and (resseq 527:604)
6X-RAY DIFFRACTION6chain 'A' and (resseq 605:657)

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