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- PDB-9b0z: Structure of Optineurin bound to HOIP NZF1 domain and M1-linked d... -

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Basic information

Entry
Database: PDB / ID: 9b0z
TitleStructure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2
Components
  • E3 ubiquitin-protein ligase RNF31
  • Optineurin
  • Ubiquitin
KeywordsSIGNALING PROTEIN / optineurin / autophagy / mitophagy / xenophagy / UBAN / NZF / HOIP / LUBAC / linear Ub chain
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / type 2 mitophagy / linear polyubiquitin binding / cell death / RBR-type E3 ubiquitin transferase / negative regulation of receptor recycling / Golgi ribbon formation / CD40 signaling pathway / positive regulation of xenophagy ...protein linear polyubiquitination / LUBAC complex / type 2 mitophagy / linear polyubiquitin binding / cell death / RBR-type E3 ubiquitin transferase / negative regulation of receptor recycling / Golgi ribbon formation / CD40 signaling pathway / positive regulation of xenophagy / protein localization to Golgi apparatus / CD40 receptor complex / Golgi to plasma membrane protein transport / negative regulation of necroptotic process / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / symbiont entry into host cell via disruption of host cell glycocalyx / 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 / symbiont entry into host cell via disruption of host cell envelope / virus tail / Golgi organization / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / 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) / negative regulation of canonical NF-kappaB signal transduction / positive regulation of autophagy / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / autophagosome / Regulation of TNFR1 signaling / ubiquitin binding / trans-Golgi network / positive regulation of NF-kappaB transcription factor activity / cytoplasmic side of plasma membrane / recycling endosome membrane / protein polyubiquitination / Regulation of PLK1 Activity at G2/M Transition / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell receptor signaling pathway / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / 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 / cytosol / cytoplasm
Similarity search - Function
NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / NEMO, Zinc finger / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / NEMO, Zinc finger / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / 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 domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tail fiber / Optineurin / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,2069
Polymers80,0767
Non-polymers1312
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.573, 72.313, 56.345
Angle α, β, γ (deg.)90.000, 95.074, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 419 through 428 and (name N...
d_2ens_1(chain "B" and ((resid 419 through 428 and (name N...
d_1ens_2(chain "C" and (resid 1 through 23 or (resid 24...
d_2ens_2(chain "D" and (resid 1 through 5 or (resid 6...
d_1ens_3(chain "E" and ((resid 353 and (name N or name...
d_2ens_3chain "F"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ASPASPALAALAAE419 - 5053 - 89
d_2ens_1ASPASPALAALABA419 - 5053 - 89
d_1ens_2METMETLEULEUCC1 - 1491 - 149
d_2ens_2METMETLEULEUDD1 - 1491 - 149
d_1ens_3ARGARGALAALAEF353 - 3794 - 30
d_2ens_3ARGARGALAALAFB353 - 3794 - 30

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.802641690309, 0.592354276602, -0.0698765194362), (0.596414472065, -0.795580827347, 0.106493777612), (0.00748962545506, -0.127151713119, -0.991855003194)10.7384961869, -31.3288243493, 22.1855576414
2given(0.834282429315, 0.546279972734, 0.0745051644265), (0.550398725174, -0.833104271084, -0.0547587146366), (0.0321569815628, 0.0866917809925, -0.995716055733)8.75484781401, -35.154732922, 33.2073430883
3given(0.756555247748, 0.652408620612, -0.0445774478467), (0.653839924249, -0.755821681203, 0.035027698766), (-0.0108402289401, -0.0556469044413, -0.998391662356)10.9314822277, -27.5925707731, 24.1724830043

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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: 11017.486 Da / Num. of mol.: 2
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/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
#3: Protein Ubiquitin


Mass: 17135.654 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.4→69.44 Å / Num. obs: 27383 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.059 / Rrim(I) all: 0.106 / Χ2: 0.79 / Net I/σ(I): 7.6
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 99.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.63 / Num. measured all: 10863 / Num. unique obs: 3582 / CC1/2: 0.733 / Rpim(I) all: 0.435 / Rrim(I) all: 0.769 / Χ2: 0.52 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→44.18 Å / SU ML: 0.3065 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2695 1257 5.03 %
Rwork0.2208 23749 -
obs0.2231 25006 64.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.98 Å2
Refinement stepCycle: LAST / Resolution: 2.41→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 2 45 4625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544623
X-RAY DIFFRACTIONf_angle_d0.8136251
X-RAY DIFFRACTIONf_chiral_restr0.0502759
X-RAY DIFFRACTIONf_plane_restr0.0055813
X-RAY DIFFRACTIONf_dihedral_angle_d24.23961730
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EAX-RAY DIFFRACTIONTorsion NCS2.56266149894
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS1.39959538963
ens_3d_2FEX-RAY DIFFRACTIONTorsion NCS1.00794410065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.50.553650.4934148X-RAY DIFFRACTION3.6
2.5-2.620.3503330.3805548X-RAY DIFFRACTION13.6
2.62-2.750.3835510.36091036X-RAY DIFFRACTION25.6
2.75-2.930.346940.31481938X-RAY DIFFRACTION47.29
2.93-3.150.32422290.29943866X-RAY DIFFRACTION95.03
3.15-3.470.32112070.2714033X-RAY DIFFRACTION99.6
3.47-3.970.27812350.20944031X-RAY DIFFRACTION98.86
3.97-50.22292160.17614036X-RAY DIFFRACTION98.49
5-44.180.25031870.20434113X-RAY DIFFRACTION97.26
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)
11.383331896031.083695254710.2332020196321.51859148093-0.07943920824710.5703964807440.0827425456084-0.385752066985-0.2485289135120.185790229733-0.134737081403-0.392951488039-0.02270199159560.0200245926621-0.0154584465233-0.0640244887379-0.2256822942840.00585961585980.2420295823550.01938885789660.211515723116-55.187370643-35.875035867112.9139970825
23.063991259251.908721704421.346051715722.181977598212.820612987484.546770231790.0835925596838-1.14584745046-2.673840608650.8263549337250.15339101019-0.9032066544871.378186568811.640894437230.7006292053410.7286588982070.0629047829377-0.2633970588711.16368399880.3508778177141.97134698061-12.0963096105-33.217986023617.1335561133
33.68832681526-0.0651565713807-1.172573752211.69729280769-0.216747969721.81402464932-0.00286913174763-0.358494280839-0.2123312096360.3724909333460.045461183906-0.2273264823750.4321293911650.5347892022480.0150720713790.271043716070.004241142629570.02566615852150.286301341309-0.003048776998920.103506456443-67.7439089405-54.730643571324.9225096803
44.173553343022.848593377722.488710761612.858290876881.954411389892.09305319271-0.175256210464-0.05632039866740.512404171642-0.134535955575-0.01852394711240.0308542500181-0.7661410485530.1006526506440.1512226999140.491945604788-0.06564646633520.09237339534870.2415994135470.0805610845990.263871885832-75.5988430201-28.04867405061.78083775674
50.0516991279586-0.09456290562070.1003349874670.646545533254-0.05605490372490.533849594659-0.04166373688940.2754570138650.2502602445930.1197684919280.106189736347-0.2183751562630.0989626182270.01584031762240.018663658059-0.0975636081062-0.222920960671-0.05271472138460.134477031363-0.1194779769490.337551807615-56.0753278561-34.306959134413.2505225544
66.80788859536-3.73128270404-0.4408552743523.691931273080.8513173068072.004707193390.2473185998850.219890426889-0.4666960773390.0289693095219-0.310140851039-0.905595791036-0.3246591463890.09294533048160.08613856491990.196559863925-0.20904302548-0.05528386683730.4765173877390.0122291938590.322230913954-20.7198484304-10.28060220077.61931698186
70.1220008758090.1513206420310.06241463281350.8183718994630.5909400365060.448553260801-0.22633659594-0.0840676694519-1.969091986940.889276122562-0.0969375795404-0.2402040880020.6524532566280.4592496712590.05163749549761.579841346510.0662606524603-0.08857345732911.014464709420.2600741338373.02087066114-16.2519313263-52.311792536219.4540988534
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 419 through 505)BA419 - 5051 - 87
22(chain 'F' and resid 353 through 379)FB353 - 3791 - 27
33(chain 'C' and resid 1 through 152)CD1 - 1521 - 152
44(chain 'D' and resid 1 through 149)DE1 - 1491 - 149
55(chain 'A' and resid 418 through 506)AF418 - 5061 - 89
66(chain 'E' and resid 353 through 379)EG353 - 3791 - 27
77(chain 'G' and resid 1 through 72)GI1 - 721 - 72

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