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- PDB-5b83: Crystal structure of Optineurin UBAN in complex with linear ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5b83
TitleCrystal structure of Optineurin UBAN in complex with linear ubiquitin
Components
  • Optineurin
  • tetra ubiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN / COILED-COIL / CELLULAR / SIGNALING / NFKB PATHWAY
Function / homology
Function and homology information


parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / cell death / negative regulation of receptor recycling / Golgi ribbon formation / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling ...parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / cell death / negative regulation of receptor recycling / Golgi ribbon formation / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Golgi organization / autophagosome / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD
Similarity search - Function
: / 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 / : / Ubiquitin domain signature. ...: / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Optineurin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.694 Å
AuthorsIshii, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2016
Title: Linear ubiquitination is involved in the pathogenesis of optineurin-associated amyotrophic lateral sclerosis
Authors: Nakazawa, S. / Oikawa, D. / Ishii, R. / Ayaki, T. / Takahashi, H. / Takeda, H. / Ishitani, R. / Kamei, K. / Takeyoshi, I. / Kawakami, H. / Iwai, K. / Hatada, I. / Sawasaki, T. / Ito, H. / ...Authors: Nakazawa, S. / Oikawa, D. / Ishii, R. / Ayaki, T. / Takahashi, H. / Takeda, H. / Ishitani, R. / Kamei, K. / Takeyoshi, I. / Kawakami, H. / Iwai, K. / Hatada, I. / Sawasaki, T. / Ito, H. / Nureki, O. / Tokunaga, F.
History
DepositionJun 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tetra ubiquitin
B: Optineurin
C: Optineurin
D: tetra ubiquitin
E: Optineurin
F: Optineurin


Theoretical massNumber of molelcules
Total (without water)114,9716
Polymers114,9716
Non-polymers00
Water1,06359
1
A: tetra ubiquitin
B: Optineurin
C: Optineurin


Theoretical massNumber of molelcules
Total (without water)57,4863
Polymers57,4863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: tetra ubiquitin
E: Optineurin
F: Optineurin


Theoretical massNumber of molelcules
Total (without water)57,4863
Polymers57,4863
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.327, 82.038, 244.853
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 tetra ubiquitin


Mass: 34253.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: 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: 11616.219 Da / Num. of mol.: 4 / Fragment: UNP residues 416-510
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.12 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 3350, 250mM Potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 40450 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 12.6
Reflection shellResolution: 2.69→2.86 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZVN

2zvn


Resolution: 2.694→49.061 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.71
RfactorNum. reflection% reflection
Rfree0.2541 2026 5.01 %
Rwork0.2012 --
obs0.2039 40445 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.694→49.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 0 59 6702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016709
X-RAY DIFFRACTIONf_angle_d1.1319014
X-RAY DIFFRACTIONf_dihedral_angle_d15.1794236
X-RAY DIFFRACTIONf_chiral_restr0.0561060
X-RAY DIFFRACTIONf_plane_restr0.0061167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6941-2.76150.38271350.30412495X-RAY DIFFRACTION92
2.7615-2.83610.31071440.2692736X-RAY DIFFRACTION100
2.8361-2.91960.35121420.24992689X-RAY DIFFRACTION100
2.9196-3.01380.30521430.23842727X-RAY DIFFRACTION100
3.0138-3.12150.31321430.23232720X-RAY DIFFRACTION100
3.1215-3.24650.29011430.23142732X-RAY DIFFRACTION100
3.2465-3.39420.23651450.21882745X-RAY DIFFRACTION100
3.3942-3.57310.28171450.20542740X-RAY DIFFRACTION100
3.5731-3.79690.26281430.22718X-RAY DIFFRACTION100
3.7969-4.08990.21821460.17882772X-RAY DIFFRACTION100
4.0899-4.50120.21791450.1642760X-RAY DIFFRACTION100
4.5012-5.15190.23041470.16812810X-RAY DIFFRACTION100
5.1519-6.48850.24981480.20652809X-RAY DIFFRACTION100
6.4885-49.06910.22081570.18762966X-RAY DIFFRACTION100
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)
18.76970.6867-3.29925.7921-1.99987.40250.4520.2544-0.249-1.2493-0.6557-0.6832-0.24891.72230.21791.09080.08320.22241.37850.17230.784.308336.82615.9629
23.67890.69840.4541.02580.05081.0459-0.09580.4441-0.2881-0.15020.0591-0.00780.1548-0.09920.02570.27430.00420.03460.5008-0.04650.469622.008142.521236.1425
31.7894-2.80182.06676.0911-3.34133.3206-0.00690.1608-0.02090.1896-0.00090.2797-0.0532-0.23890.01470.1619-0.00440.05570.3828-0.01130.417354.64836.185450.8371
43.5407-1.82744.36710.7715-1.30944.9155-0.26430.28920.3976-0.1894-0.0435-0.094-0.6077-0.2940.29570.38790.0374-0.02450.63570.06760.418763.16641.531335.1132
56.8324-1.92196.23571.4611-1.67.87680.36451.3139-0.2011-0.3267-0.3810.03520.3540.7205-0.02680.24650.02350.07050.5702-0.03490.448266.810335.785736.8975
63.61310.70411.61324.19832.3144.22390.26881.97010.0403-1.22820.0068-0.1986-0.04-0.6221-0.22560.74180.138-0.05561.2083-0.01280.502274.87388.093821.5101
74.80522.2757-2.93744.8386-2.39922.20810.01570.14460.1017-0.20680.08560.12710.0312-0.1782-0.12210.28670.0169-0.10070.2716-0.01760.261759.69674.391846.6434
81.9646-3.2687-1.65467.4913.59972.67330.0703-0.12210.2024-0.21220.1531-0.4499-0.19860.2232-0.20820.21710.0021-0.0180.313-0.00350.392127.97096.664251.7702
90.20860.32920.01627.69862.17060.6399-0.18842.1257-0.1193-2.31531.12211.11810.8004-1.2896-0.80911.53390.2137-0.20191.8480.01820.656322.5679-4.564717.8343
108.1526-5.6949-7.81036.51357.02158.32670.4734-0.14050.3102-0.54230.139-0.0719-1.04740.6708-0.35790.23870.0114-0.07480.36790.03820.41288.948813.654949.7996
116.7678-4.055-6.21812.67072.84745.5985-0.1902-0.1557-0.6779-0.2615-0.05080.27950.59320.53930.18620.41020.0942-0.13620.5724-0.08830.596914.54163.465742.184
124.62550.5192-5.81490.5001-1.18778.2611.22690.72022.4661-0.1149-0.03570.6838-0.2741-1.1365-1.16650.38650.13680.17510.54870.16540.7829-17.583618.857171.4747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 302 )
4X-RAY DIFFRACTION4chain 'B' and (resid 443 through 501 )
5X-RAY DIFFRACTION5chain 'C' and (resid 445 through 505 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 77 )
7X-RAY DIFFRACTION7chain 'D' and (resid 78 through 153 )
8X-RAY DIFFRACTION8chain 'D' and (resid 154 through 300 )
9X-RAY DIFFRACTION9chain 'E' and (resid 453 through 460 )
10X-RAY DIFFRACTION10chain 'E' and (resid 461 through 502 )
11X-RAY DIFFRACTION11chain 'F' and (resid 447 through 499 )
12X-RAY DIFFRACTION12chain 'F' and (resid 500 through 505 )

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