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- PDB-5ep6: The crystal structure of NAP1 in complex with TBK1 -

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Basic information

Entry
Database: PDB / ID: 5ep6
TitleThe crystal structure of NAP1 in complex with TBK1
Components
  • 5-azacytidine-induced protein 2
  • Serine/threonine-protein kinase TBK1
KeywordsPROTEIN BINDING/TRANSFERASE / NAP1 / TBK1 / CALCOCO2 / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / dendritic cell differentiation / 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 activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / dendritic cell differentiation / 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 / negative regulation of canonical NF-kappaB signal transduction / negative regulation of TORC1 signaling / positive regulation of autophagy / antiviral innate immune response / positive regulation of TORC1 signaling / peptidyl-threonine phosphorylation / 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 / T cell activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / macroautophagy / Regulation of TNFR1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / SARS-CoV-1 activates/modulates innate immune responses / mitotic cell cycle / peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / protein phosphatase binding / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / nucleic acid binding / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of canonical NF-kappaB signal transduction / 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 / innate immune response / negative regulation of gene expression / 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
: / Tbk1/Ikki binding domain / TBD domain / 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 / : / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...: / Tbk1/Ikki binding domain / TBD domain / 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 / : / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
5-azacytidine-induced protein 2 / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.451 Å
AuthorsLi, F. / Xie, X. / Liu, J. / Pan, L.
Funding support China, 2items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31470749 China
National Basic Research Program of China2013CB836900 China
CitationJournal: Nat Commun / Year: 2016
Title: Structural insights into the interaction and disease mechanism of neurodegenerative disease-associated optineurin and TBK1 proteins.
Authors: Li, F. / Xie, X. / Wang, Y. / Liu, J. / Cheng, X. / Guo, Y. / Gong, Y. / Hu, S. / Pan, L.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-azacytidine-induced protein 2
C: 5-azacytidine-induced protein 2
B: Serine/threonine-protein kinase TBK1
D: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3729
Polymers23,9114
Non-polymers4605
Water1,820101
1
A: 5-azacytidine-induced protein 2
B: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1404
Polymers11,9562
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-18 kcal/mol
Surface area7030 Å2
MethodPISA
2
C: 5-azacytidine-induced protein 2
D: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2325
Polymers11,9562
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-22 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 50.113, 84.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide 5-azacytidine-induced protein 2 / NF-kappa-B-activating kinase-associated protein 1 / Nak-associated protein 1 / TILP


Mass: 5631.463 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 215-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZI2, NAP1, TBKBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6S1
#2: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 6324.202 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 677-729
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% w/v Tryptone, 0.05 M HEPES sodium (pH 7.0), 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 298.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 31428 / % possible obs: 98.77 % / Redundancy: 6.8 % / Net I/σ(I): 27.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.451→43.092 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1583 5.05 %
Rwork0.1867 --
obs0.1883 31329 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→43.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 30 101 1430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061541
X-RAY DIFFRACTIONf_angle_d0.9942090
X-RAY DIFFRACTIONf_dihedral_angle_d17.787638
X-RAY DIFFRACTIONf_chiral_restr0.06232
X-RAY DIFFRACTIONf_plane_restr0.003266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4507-1.49750.24111300.20422394X-RAY DIFFRACTION89
1.4975-1.55110.25691430.17152687X-RAY DIFFRACTION99
1.5511-1.61320.20331400.15872738X-RAY DIFFRACTION100
1.6132-1.68660.20671420.15132688X-RAY DIFFRACTION100
1.6866-1.77550.23091680.15352691X-RAY DIFFRACTION100
1.7755-1.88680.20611370.16422729X-RAY DIFFRACTION100
1.8868-2.03240.23021300.16162744X-RAY DIFFRACTION100
2.0324-2.2370.17821480.15472744X-RAY DIFFRACTION100
2.237-2.56060.19111530.17162747X-RAY DIFFRACTION100
2.5606-3.2260.23781490.19992796X-RAY DIFFRACTION100
3.226-43.11090.22561430.21462788X-RAY DIFFRACTION95

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