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- PDB-5eof: Crystal structure of OPTN NTD and TBK1 CTD complex -

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Basic information

Entry
Database: PDB / ID: 5eof
TitleCrystal structure of OPTN NTD and TBK1 CTD complex
Components
  • Optineurin
  • Serine/threonine-protein kinase TBK1
KeywordsPROTEIN BINDING/TRANSFERASE / OPTN / TBK1 / ALS / autophagy / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / negative regulation of receptor recycling / cell death / STAT6-mediated induction of chemokines / protein localization to Golgi apparatus / positive regulation of xenophagy / serine/threonine protein kinase complex / Golgi to plasma membrane protein transport ...IRF3 mediated activation of type 1 IFN / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / negative regulation of receptor recycling / cell death / STAT6-mediated induction of chemokines / protein localization to Golgi apparatus / positive regulation of xenophagy / serine/threonine protein kinase complex / Golgi to plasma membrane protein transport / 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 / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / Golgi organization / positive regulation of interferon-alpha production / antiviral innate immune response / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / autophagosome / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / cellular response to unfolded protein / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / TICAM1-dependent activation of IRF3/IRF7 / 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) / TNFR1-induced NF-kappa-B signaling pathway / 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 / trans-Golgi network / autophagy / recycling endosome membrane / SARS-CoV-1 activates/modulates innate immune responses / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / positive regulation of peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / peptidyl-serine phosphorylation / protein phosphatase binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / Potential therapeutics for SARS / nucleic acid binding / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / inflammatory response / Golgi membrane / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / intracellular membrane-bounded organelle / innate immune response / protein serine/threonine kinase activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / 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 / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ 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 / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / 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
Optineurin / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsLi, F. / Xie, X. / Liu, J. / Pan, L.
Funding support China, 2items
OrganizationGrant numberCountry
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 10, 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: Optineurin
B: Optineurin
C: Serine/threonine-protein kinase TBK1
D: Serine/threonine-protein kinase TBK1


Theoretical massNumber of molelcules
Total (without water)31,7964
Polymers31,7964
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-95 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.321, 54.775, 153.141
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 Optineurin / / E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein ...E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein 7 / HIP-7 / Huntingtin-interacting protein L / NEMO-related protein / Optic neuropathy-inducing protein / Transcription factor IIIA-interacting protein / TFIIIA-IntP


Mass: 9650.888 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CV9
#2: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 6247.161 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES monohydrate pH 6.0, 14% w/v polyethylene glycol 4000

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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 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 19991 / % possible obs: 99.9 % / Redundancy: 6.4 % / Net I/σ(I): 14.85

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.05→37.344 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 1020 5.11 %
Rwork0.2075 --
obs0.2094 19973 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 0 98 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071949
X-RAY DIFFRACTIONf_angle_d0.962610
X-RAY DIFFRACTIONf_dihedral_angle_d16.657788
X-RAY DIFFRACTIONf_chiral_restr0.062289
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.049-2.1570.28511420.25282656X-RAY DIFFRACTION100
2.157-2.29210.34231390.2332666X-RAY DIFFRACTION100
2.2921-2.46910.29041560.22982640X-RAY DIFFRACTION100
2.4691-2.71750.28251430.22422676X-RAY DIFFRACTION100
2.7175-3.11060.30651310.23462713X-RAY DIFFRACTION100
3.1106-3.91830.25261430.19782747X-RAY DIFFRACTION100
3.9183-37.35030.19291660.18792855X-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)
12.1777-3.4854-0.08718.41710.66420.10520.19920.0891-0.0528-0.4646-0.00690.90720.02360.0419-0.18431.0148-0.1242-0.0245-0.02090.16050.428-3.840620.7277-59.8366
20.4398-0.3077-0.97030.74931.80476.7113-0.1756-0.1027-0.04520.06670.08110.06350.71840.22690.06780.2214-0.01010.0370.2034-0.0220.27852.33536.9235-11.7019
33.8877-4.54910.13815.395-0.54353.6030.35120.52910.6336-0.1584-0.3855-1.0252-0.64410.90780.090.5658-0.07420.10430.4345-0.04540.49875.3913-4.4745-60.5362
40.1077-0.3344-0.63650.34340.31032.4731-0.0338-0.01780.0147-0.12420.04070.024-0.1613-0.02250.03050.2778-0.02480.02350.3046-0.05110.2577-5.80148.793-13.6432
50.5239-0.27840.93591.674-1.29652.02950.0369-0.0999-0.1091-0.28190.12550.271-0.7232-0.4031-0.14410.37870.0264-0.02370.21530.04330.3162-2.423713.725-35.6328
60.7861-0.4543-0.81351.77240.28587.1942-0.11980.08780.0036-0.20680.1737-0.05761.1755-0.0676-0.05280.3459-0.08480.02550.2134-0.11320.35971.89851.835-35.8511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 102 )
3X-RAY DIFFRACTION3chain 'B' and (resid 29 through 36 )
4X-RAY DIFFRACTION4chain 'B' and (resid 37 through 102 )
5X-RAY DIFFRACTION5chain 'C' and (resid 678 through 720 )
6X-RAY DIFFRACTION6chain 'D' and (resid 679 through 719 )

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