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- PDB-5eoa: Crystal structure of OPTN E50K mutant and TBK1 complex -

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Basic information

Entry
Database: PDB / ID: 5eoa
TitleCrystal structure of OPTN E50K mutant and TBK1 complex
Components
  • Optineurin
  • Serine/threonine-protein kinase TBK1
KeywordsPROTEIN BINDING/TRANSFERASE / Optineurin / TBK1 / POAG / ALS / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / negative regulation of receptor recycling / type 2 mitophagy / cell death / Golgi ribbon formation / STAT6-mediated induction of chemokines / protein localization to Golgi apparatus / positive regulation of xenophagy / serine/threonine protein kinase complex / regulation of type I interferon production ...IRF3 mediated activation of type 1 IFN / negative regulation of receptor recycling / type 2 mitophagy / cell death / Golgi ribbon formation / STAT6-mediated induction of chemokines / protein localization to Golgi apparatus / positive regulation of xenophagy / serine/threonine protein kinase complex / regulation of type I interferon production / dendritic cell proliferation / Golgi to plasma membrane protein transport / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / Interleukin-37 signaling / positive regulation of type I interferon-mediated signaling pathway / TBC/RABGAPs / cytoplasmic pattern recognition receptor signaling pathway / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / K63-linked polyubiquitin modification-dependent protein binding / type I interferon-mediated signaling pathway / Golgi organization / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / canonical NF-kappaB signal transduction / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / activation of innate immune response / antiviral innate immune response / negative 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 / positive regulation of interferon-beta production / positive regulation of TORC1 signaling / autophagosome / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / peptidyl-threonine phosphorylation / phosphoprotein binding / Regulation of TNFR1 signaling / trans-Golgi network / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / autophagy / recycling endosome membrane / SARS-CoV-1 activates/modulates innate immune responses / Regulation of PLK1 Activity at G2/M Transition / positive regulation of peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / protein-macromolecule adaptor activity / 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 / protein phosphorylation / Golgi membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / protein serine kinase activity / 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 / nucleus / metal ion 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 / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. ...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 / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / 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: 2.503 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
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-95 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.824, 54.549, 153.305
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: 9650.953 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-103 / Mutation: E50K
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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291.5 K / Method: evaporation / pH: 6
Details: 0.1M MES monohydrate pH 6.0, 14% w/V Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 291.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11226 / % possible obs: 99.72 % / Redundancy: 3.5 % / Net I/σ(I): 10.42

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.503→44.444 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 535 4.77 %
Rwork0.1988 --
obs0.2018 11206 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→44.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 0 24 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071913
X-RAY DIFFRACTIONf_angle_d0.8962549
X-RAY DIFFRACTIONf_dihedral_angle_d18.473778
X-RAY DIFFRACTIONf_chiral_restr0.057281
X-RAY DIFFRACTIONf_plane_restr0.003327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5031-2.7550.37531370.25992572X-RAY DIFFRACTION99
2.755-3.15350.28491450.23442634X-RAY DIFFRACTION100
3.1535-3.97270.28621240.19892670X-RAY DIFFRACTION100
3.9727-44.45090.22131290.17612795X-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)
13.7403-2.3807-1.01677.21732.74795.85760.6270.96080.04890.2175-0.2173-0.2465-1.74250.3722-0.5450.8781-0.0155-0.08540.5037-0.09770.55871.9548-19.9356-59.6639
20.3912-0.32371.22681.0881-1.67628.226-0.1661-0.1348-0.00480.11510.0930.0222-0.7642-0.6570.1360.309-0.0185-0.00210.42510.06010.496-2.0185-6.9512-12.1683
34.7894-4.722.72644.6703-2.41075.62050.70720.0521-0.3069-0.5205-0.06510.43231.2835-1.0687-0.60670.7782-0.11870.02120.5767-0.02560.6621-6.68284.3607-59.0279
40.3637-0.31690.66790.62-0.18542.5803-0.2877-0.0257-0.0316-0.0404-0.2378-0.1151-0.27510.54820.53720.3404-0.0343-0.03310.48530.05620.51666.1827-8.7288-14.0029
50.2244-0.0004-0.73222.3346-0.54072.3538-0.0117-0.0587-0.0016-0.34790.0967-0.23591.01970.4529-0.03210.42740.00950.04430.4118-0.05190.47352.3573-13.7001-36.1225
61.1694-0.54293.33151.2282-1.28619.4848-0.4126-0.03060.11630.00680.1680.0907-1.5773-0.09750.17350.4707-0.0591-0.01950.40390.11190.5261-2.0181-1.8388-35.5943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 101 )
3X-RAY DIFFRACTION3chain 'B' and (resid 30 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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