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- PDB-4im3: Structure of Tank-Binding Kinase 1 -

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Basic information

Entry
Database: PDB / ID: 4im3
TitleStructure of Tank-Binding Kinase 1
ComponentsSerine/threonine-protein kinase TBK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / serine/threonine kinase / BX795 / pCMNP / 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 / type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / positive regulation of macroautophagy / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / positive regulation of autophagy / negative regulation of TORC1 signaling / antiviral innate immune response / positive regulation of TORC1 signaling / 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 / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy / peptidyl-threonine phosphorylation / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / macroautophagy / Regulation of TNFR1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / SARS-CoV-1 activates/modulates innate immune responses / TRAF3-dependent IRF activation pathway / peptidyl-serine phosphorylation / protein phosphatase binding / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / nucleic acid binding / eukaryotic translation initiation factor 2alpha kinase activity / 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 / 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: 3.342 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 / Refinement description
Category: citation / citation_author / software
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 / _software.classification / _software.name / _software.version
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_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_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,8158
Polymers76,1851
Non-polymers1,6307
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)155,63016
Polymers152,3702
Non-polymers3,26014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area5930 Å2
ΔGint-264 kcal/mol
Surface area60500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.320, 141.320, 85.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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-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
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4% MPD, 100 mM Hepes pH 7.0, 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: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2011
RadiationMonochromator: MD2 micro-diffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 15314 / Num. obs: 13368 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.3-3.63151.5
3.63-4.16199.4
4.16-5.24199.1
5.24-50198.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.342→40.796 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 684 5.12 %random
Rwork0.2196 ---
all0.2226 14554 --
obs0.2226 13358 91.78 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99.446 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--20.7228 Å20 Å20 Å2
2---20.7228 Å20 Å2
3---41.4456 Å2
Refinement stepCycle: LAST / Resolution: 3.342→40.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4849 0 40 0 4889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065021
X-RAY DIFFRACTIONf_angle_d1.2136782
X-RAY DIFFRACTIONf_dihedral_angle_d15.4131878
X-RAY DIFFRACTIONf_chiral_restr0.056752
X-RAY DIFFRACTIONf_plane_restr0.005861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.342-3.59990.41611180.30341687X-RAY DIFFRACTION63
3.5999-3.96190.2811600.24732695X-RAY DIFFRACTION100
3.9619-4.53460.22341280.1952742X-RAY DIFFRACTION99
4.5346-5.71060.26431370.20132755X-RAY DIFFRACTION99
5.7106-40.79860.28481410.22072795X-RAY DIFFRACTION98
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)
16.5158-3.9774-1.52156.2181.03862.84650.03190.7868-1.2225-0.894-0.18760.05270.8139-0.44230.05781.0348-0.07640.18050.2974-0.01510.8167111.030718.2641-31.5475
26.69422.31680.67075.1681-0.09264.91360.187-0.5859-2.65190.6665-0.23120.26670.343-0.7311-0.08240.8752-0.00180.1960.97240.321.459290.62417.6433-10.7186
33.585-1.5890.01924.93141.71440.33120.0368-0.0651-0.5915-0.9258-0.18650.8139-0.3525-0.24070.1250.97590.26990.05790.78290.11640.558694.808246.888-14.3881
48.8849-6.60192.97979.5843-4.92375.9153-0.783-0.65421.38211.75240.86760.0993-0.26470.043-0.00710.9460.20510.01530.8651-0.20690.940979.825392.8876-2.9869
54.8904-1.74921.11886.6859-0.43990.568-0.3702-0.689-0.6405-0.15180.244-0.940.2140.16150.14990.9630.20810.32111.04590.42960.8564114.878931.88770.9246
63.603-1.62881.44263.1858-0.40021.4818-1.19-0.53610.04210.56930.47920.6602-0.1693-0.10870.40531.08850.55960.40081.1845-0.19560.448284.109973.4323-5.3711
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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