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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 / CD40 signaling pathway / Golgi ribbon formation / 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 / CD40 signaling pathway / Golgi ribbon formation / positive regulation of xenophagy / protein localization to Golgi apparatus / CD40 receptor complex / negative regulation of necroptotic process / Golgi to plasma membrane protein transport / hypothalamus gonadotrophin-releasing hormone neuron development / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / female meiosis I / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / fat pad development / mitochondrion transport along microtubule / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / Golgi organization / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of canonical NF-kappaB signal transduction / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / positive regulation of autophagy / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / autophagosome / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / regulation of mitochondrial membrane potential
Similarity search - Function
E3 ubiquitin-protein ligase RNF31, UBA domain / NF-kappa-B essential modulator NEMO, N-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 / : / : / : / : ...E3 ubiquitin-protein ligase RNF31, UBA domain / NF-kappa-B essential modulator NEMO, N-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 / : / : / : / : / : / : / NF-kappa-B essential modulator NEMO / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / C2H2 type zinc-finger / PNGase/UBA- or UBX-containing domain / 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 domain / PUB-like domain superfamily / PUB domain / IBR 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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / 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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