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- PDB-9b0b: Structure of Optineurin bound to HOIP NZF1 domain -

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Basic information

Entry
Database: PDB / ID: 9b0b
TitleStructure of Optineurin bound to HOIP NZF1 domain
Components
  • E3 ubiquitin-protein ligase RNF31
  • Optineurin
KeywordsSIGNALING PROTEIN / optineurin / autophagy / mitophagy / xenophagy / UBAN / NZF / HOIP / LUBAC / linear Ub chain
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / linear polyubiquitin binding / CD40 signaling pathway / cell death / negative regulation of receptor recycling / Golgi ribbon formation / RBR-type E3 ubiquitin transferase / protein localization to Golgi apparatus ...protein linear polyubiquitination / LUBAC complex / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / linear polyubiquitin binding / CD40 signaling pathway / cell death / negative regulation of receptor recycling / Golgi ribbon formation / RBR-type E3 ubiquitin transferase / protein localization to Golgi apparatus / positive regulation of xenophagy / CD40 receptor complex / Golgi to plasma membrane protein transport / negative regulation of necroptotic process / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / 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 / 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 IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / trans-Golgi network / cytoplasmic side of plasma membrane / autophagy / protein polyubiquitination / recycling endosome membrane / ubiquitin-protein transferase activity / Regulation of PLK1 Activity at G2/M Transition / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / defense response to bacterium / Golgi membrane / innate immune response / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : ...: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / C2H2 type zinc-finger / PNGase/UBA- or UBX-containing domain / 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 / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Optineurin / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMichel, M.A. / Scutts, S. / Komander, D.
Funding support United Kingdom, European Union, Australia, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192732 United Kingdom
European Research Council (ERC)724804European Union
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
CitationJournal: To Be Published
Title: Linkage and substrate specificity conferred by NZF ubiquitin binding domains
Authors: Michel, M.A. / Scutts, S. / Komander, D.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Optineurin
B: Optineurin
G: E3 ubiquitin-protein ligase RNF31
C: Optineurin
D: Optineurin
E: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,82820
Polymers50,8076
Non-polymers2,02114
Water5,098283
1
A: Optineurin
B: Optineurin
G: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,41410
Polymers25,4043
Non-polymers1,0107
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Optineurin
D: Optineurin
E: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,41410
Polymers25,4043
Non-polymers1,0107
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.755, 92.684, 149.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDGE

#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: 11043.457 Da / Num. of mol.: 4 / Fragment: Optineurin UBAN domain, residues 419-512 / Mutation: C472S, S473E
Source method: isolated from a genetically manipulated source
Details: Mutations C472S, S473E to improve protein yield / Source: (gene. exp.) Homo sapiens (human) / Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CV9
#2: Protein/peptide E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 3316.815 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase

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Non-polymers , 4 types, 297 molecules

#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 3:1 (protein:mother liquor: 10% PEG 8K, 20% ethylene glycol, 0.1 M Tris/Bicine pH 8.5, 0.03 M MgCl2 and 0.03 M CaCl2. cryoprotected in mother liquor containing 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 1.7→78.82 Å / Num. obs: 77197 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Rrim(I) all: 0.088 / Χ2: 0.9 / Net I/σ(I): 12.1 / Num. measured all: 493784
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.83 / Num. measured all: 25734 / Num. unique obs: 4026 / CC1/2: 0.592 / Rpim(I) all: 0.355 / Rrim(I) all: 0.904 / Χ2: 0.69 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→58.265 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 3985 5.17 %5%
Rwork0.1961 ---
obs0.1974 77092 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→58.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 110 283 3500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163391
X-RAY DIFFRACTIONf_angle_d1.5274536
X-RAY DIFFRACTIONf_dihedral_angle_d10.4733030
X-RAY DIFFRACTIONf_chiral_restr0.086517
X-RAY DIFFRACTIONf_plane_restr0.008585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.36081530.32192556X-RAY DIFFRACTION100
1.7207-1.74250.30041640.30342536X-RAY DIFFRACTION100
1.7425-1.76540.32971260.28842590X-RAY DIFFRACTION100
1.7654-1.78960.26891340.28142605X-RAY DIFFRACTION100
1.7896-1.81520.26411450.27122580X-RAY DIFFRACTION100
1.8152-1.84230.28881470.26562562X-RAY DIFFRACTION100
1.8423-1.87110.24221350.27242579X-RAY DIFFRACTION100
1.8711-1.90180.30551210.2662597X-RAY DIFFRACTION100
1.9018-1.93460.27021540.24152571X-RAY DIFFRACTION100
1.9346-1.96970.28061270.23322598X-RAY DIFFRACTION100
1.9697-2.00760.21851380.21872572X-RAY DIFFRACTION100
2.0076-2.04860.25011670.20942559X-RAY DIFFRACTION100
2.0486-2.09320.25091270.20572620X-RAY DIFFRACTION100
2.0932-2.14180.21791230.19392613X-RAY DIFFRACTION100
2.1418-2.19540.23851350.19252599X-RAY DIFFRACTION100
2.1954-2.25480.22621800.18512569X-RAY DIFFRACTION100
2.2548-2.32110.21461190.18632600X-RAY DIFFRACTION100
2.3211-2.3960.21511500.17832591X-RAY DIFFRACTION100
2.396-2.48170.22181290.18512653X-RAY DIFFRACTION100
2.4817-2.5810.20251430.17142594X-RAY DIFFRACTION100
2.581-2.69850.24211170.182623X-RAY DIFFRACTION100
2.6985-2.84080.19391410.18072636X-RAY DIFFRACTION100
2.8408-3.01880.22681520.18692620X-RAY DIFFRACTION100
3.0188-3.25180.21771570.19572617X-RAY DIFFRACTION100
3.2518-3.5790.17621470.17732666X-RAY DIFFRACTION100
3.579-4.09680.17051530.15732655X-RAY DIFFRACTION100
4.0968-5.16110.18471230.16592729X-RAY DIFFRACTION100
5.1611-58.2650.25431780.22022817X-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)
10.44710.5318-1.97140.2955-1.67347.012-0.09760.0378-0.0634-0.03990.0435-0.01250.269-0.2188-0.00920.3060.05310.03020.25110.04570.228515.8482-30.36885.4043
20.44530.6774-1.7550.7788-2.58715.79670.0763-0.0792-0.027-0.02450.04030.06610.0160.1397-0.00820.2968-0.00340.02150.25550.06340.225314.8753-31.89076.2021
35.4414-1.53832.53423.31490.61675.0767-0.0621-1.4094-0.80011.51170.0464-0.11331.1182-0.09690.02390.4129-0.00850.00450.3260.15910.327618.4559-48.429648.4911
47.3523-3.273-4.75054.32162.77374.953-0.0798-0.4052-0.17950.2195-0.0162-0.24790.06950.28550.11990.1671-0.0157-0.02160.18460.11490.279521.1623-44.971543.1286
57.5313-0.02410.41572.72553.29624.2593-0.00690.09240.08780.0075-0.1314-0.3756-0.09130.18040.05820.16320.0168-0.01460.15110.10420.246417.7248-42.488739.4955
60.85011.27483.07451.16213.33157.9882-0.10640.0210.0351-0.13960.06450.0197-0.37020.02090.01010.30490.0643-0.05990.3051-0.11780.24747.8893-14.63824.8664
71.09651.44772.65582.71935.01189.15160.1318-0.1373-0.0348-0.05810.0713-0.239-0.1048-0.2348-0.13620.20560.0235-0.01880.1364-0.03850.20648.4715-13.29036.1334
80.1533-0.9631-0.10866.4533-0.39384.4225-0.3097-0.9550.59040.94660.1353-0.5749-0.57250.16330.10840.3020.072-0.11290.5414-0.25370.436.662910.213544.6142
96.5606-3.1132-2.94213.868-1.79758.6665-0.0085-0.09240.34320.0609-0.04230.0746-0.10440.03830.09370.18110.012-0.01690.2004-0.07180.27152.70738.665833.6701
103.4096-4.12551.74955.1009-1.85641.2864-0.407-0.75790.21560.75360.23040.0884-0.1652-0.11760.06350.2210.048-0.01090.2577-0.1350.25724.32825.418642.8173
116.32190.0991-0.4132.8325-1.41624.2319-0.0510.2705-0.0599-0.0109-0.01690.00060.1213-0.01270.04880.16470.0591-0.02150.1627-0.07810.26957.17913.584336.0114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 420 through 504 )
2X-RAY DIFFRACTION2chain 'B' and (resid 419 through 501 )
3X-RAY DIFFRACTION3chain 'G' and (resid 351 through 355 )
4X-RAY DIFFRACTION4chain 'G' and (resid 356 through 370 )
5X-RAY DIFFRACTION5chain 'G' and (resid 371 through 379 )
6X-RAY DIFFRACTION6chain 'C' and (resid 420 through 502 )
7X-RAY DIFFRACTION7chain 'D' and (resid 417 through 502 )
8X-RAY DIFFRACTION8chain 'E' and (resid 351 through 355 )
9X-RAY DIFFRACTION9chain 'E' and (resid 356 through 360 )
10X-RAY DIFFRACTION10chain 'E' and (resid 361 through 370 )
11X-RAY DIFFRACTION11chain 'E' and (resid 371 through 379 )

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