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- PDB-4jlc: Crystal structure of mouse TBK1 bound to SU6668 -

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Basic information

Entry
Database: PDB / ID: 4jlc
TitleCrystal structure of mouse TBK1 bound to SU6668
ComponentsSerine/threonine-protein kinase TBK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Interleukin-37 signaling / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TNFR1-induced proapoptotic signaling / Negative regulators of DDX58/IFIH1 signaling / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of TNFR1 signaling / positive regulation of xenophagy ...Interleukin-37 signaling / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TNFR1-induced proapoptotic signaling / Negative regulators of DDX58/IFIH1 signaling / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of TNFR1 signaling / positive regulation of xenophagy / dendritic cell proliferation / regulation of type I interferon production / positive regulation of type I interferon-mediated signaling pathway / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / antiviral innate immune response / positive regulation of interferon-alpha production / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / activation of innate immune response / positive regulation of interferon-beta production / phosphoprotein binding / peptidyl-threonine phosphorylation / regulation of gene expression / peptidyl-serine phosphorylation / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / nucleic acid binding / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / protein phosphorylation / negative regulation of gene expression / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
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-SU6 / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, P.
CitationJournal: Structure / Year: 2013
Title: Structural Insights into the Functions of TBK1 in Innate Antimicrobial Immunity.
Authors: Shu, C. / Sankaran, B. / Chaton, C.T. / Herr, A.B. / Mishra, A. / Peng, J. / Li, P.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)76,0012
Polymers75,6901
Non-polymers3101
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)152,0014
Polymers151,3812
Non-polymers6212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4670 Å2
ΔGint-23 kcal/mol
Surface area67650 Å2
MethodPISA
2
A: Serine/threonine-protein kinase TBK1
hetero molecules

A: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0014
Polymers151,3812
Non-polymers6212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4370 Å2
ΔGint-3 kcal/mol
Surface area67950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.480, 140.480, 86.560
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 / T2K / TANK-binding kinase 1


Mass: 75690.375 Da / Num. of mol.: 1
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: Chemical ChemComp-SU6 / 3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid / SU6668


Mass: 310.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3

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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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Sodium Citrate, 0.1 M HEPES, 10-14% isopropanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2013
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→70.53 Å / Num. all: 20027 / Num. obs: 20027 / % possible obs: 100 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 10.4 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EUT AND 3QA8

4eut

3qa8


Resolution: 3→70.53 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1994 9.96 %random
Rwork0.2335 ---
all0.237 20027 --
obs0.2368 20015 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→70.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5230 0 23 0 5253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045361
X-RAY DIFFRACTIONf_angle_d0.8267236
X-RAY DIFFRACTIONf_dihedral_angle_d16.6982017
X-RAY DIFFRACTIONf_chiral_restr0.062797
X-RAY DIFFRACTIONf_plane_restr0.003923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.40441390.34631256X-RAY DIFFRACTION100
3.075-3.15820.31581420.3291266X-RAY DIFFRACTION100
3.1582-3.25110.31971410.3161271X-RAY DIFFRACTION100
3.2511-3.3560.3171440.29061277X-RAY DIFFRACTION100
3.356-3.4760.31131380.26591287X-RAY DIFFRACTION100
3.476-3.61520.31621390.25921263X-RAY DIFFRACTION100
3.6152-3.77970.27351460.2461286X-RAY DIFFRACTION100
3.7797-3.97890.28481420.23221274X-RAY DIFFRACTION100
3.9789-4.22820.28161390.22531288X-RAY DIFFRACTION100
4.2282-4.55460.25811430.20581291X-RAY DIFFRACTION100
4.5546-5.01280.22841440.2091283X-RAY DIFFRACTION100
5.0128-5.73790.28451440.23391301X-RAY DIFFRACTION100
5.7379-7.2280.28621440.26421318X-RAY DIFFRACTION100
7.228-70.54930.22251490.20091360X-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)
15.70451.6219-1.14673.41970.28783.2443-0.2343-0.7599-1.62220.9727-0.14690.11690.73030.5510.18090.9572-0.00210.17940.570.17840.936329.007917.550319.2686
20.2346-0.480.14811.1424-0.32770.0501-0.19530.97150.6743-0.32420.1853-1.0444-0.1376-0.4495-0.14341.44010.01690.06560.95730.23551.488347.45840.779520.311
38.5024-3.33971.87139.0514.61688.1515-0.30440.6472-0.8804-0.0588-1.1193-0.83191.9977-0.08781.17730.889-0.14460.40440.911-0.12021.001145.56117.77592.4149
41.94840.6091-0.27453.2243-0.9512-0.37110.0424-0.0023-0.01980.4441-0.1192-0.7719-0.24930.44170.1251.0632-0.50440.09460.9574-0.16440.722849.838151.8803-2.2046
53.15322.7522.4545.11941.91860.8742-0.93920.76550.0224-1.03980.68890.1089-0.30540.42590.28720.9166-0.47980.37960.8788-0.21810.525638.739348.9129-13.1902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 155 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 201 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 524 )
5X-RAY DIFFRACTION5chain 'A' and (resid 525 through 656 )

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