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- PDB-4efo: Crystal structure of the ubiquitin-like domain of human TBK1 -

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Basic information

Entry
Database: PDB / ID: 4efo
TitleCrystal structure of the ubiquitin-like domain of human TBK1
ComponentsSerine/threonine-protein kinase TBK1
KeywordsTRANSFERASE / ubiquitin like domain
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 / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated 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 / activation of innate immune response / positive regulation of interferon-beta production / 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 / innate immune response / protein serine kinase activity / 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
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site ...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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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 / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.769 Å
AuthorsLi, J. / Li, J. / Miyahira, A. / Sun, J. / Liu, Y. / Cheng, G. / Liang, H.
CitationJournal: Protein Cell / Year: 2012
Title: Crystal structure of the ubiquitin-like domain of human TBK1.
Authors: Li, J. / Li, J. / Miyahira, A. / Sun, J. / Liu, Y. / Cheng, G. / Liang, H.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)21,8832
Polymers21,8832
Non-polymers00
Water3,855214
1
A: Serine/threonine-protein kinase TBK1


Theoretical massNumber of molelcules
Total (without water)10,9421
Polymers10,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase TBK1


Theoretical massNumber of molelcules
Total (without water)10,9421
Polymers10,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.353, 47.785, 61.832
Angle α, β, γ (deg.)90.00, 93.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10941.543 Da / Num. of mol.: 2 / Fragment: ubiquitin-like domain, UNP RESIDUE 302-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBK1, NAK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UHD2, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M BIS-TRIS,0.2M NaCl,21% PEG 3350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 18, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.769→50 Å / Num. all: 19689 / Num. obs: 19650 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.77→1.8 Å / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.769→30.857 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1004 5.12 %
Rwork0.1695 --
obs0.1713 19627 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.159 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0962 Å2-0 Å22.0024 Å2
2--0.945 Å2-0 Å2
3---3.1512 Å2
Refinement stepCycle: LAST / Resolution: 1.769→30.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 0 214 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061434
X-RAY DIFFRACTIONf_angle_d1.0151942
X-RAY DIFFRACTIONf_dihedral_angle_d13.744521
X-RAY DIFFRACTIONf_chiral_restr0.069226
X-RAY DIFFRACTIONf_plane_restr0.004241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7695-1.86270.25561340.1859260698
1.8627-1.97940.21181500.16812627100
1.9794-2.13220.2121510.15872656100
2.1322-2.34670.21571340.16662660100
2.3467-2.68610.22291310.18032690100
2.6861-3.38360.22051480.17552662100
3.3836-30.86190.17171560.15892722100

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