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- PDB-9b0z: Structure of Optineurin bound to HOIP NZF1 domain and M1-linked d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9b0z | ||||||||||||
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Title | Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 | ||||||||||||
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![]() | SIGNALING PROTEIN / optineurin / autophagy / mitophagy / xenophagy / UBAN / NZF / HOIP / LUBAC / linear Ub chain | ||||||||||||
Function / homology | ![]() 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 / 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 / mitochondrion transport along microtubule / fat pad development / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / Golgi organization / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / autophagosome / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / positive regulation of autophagy / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / energy homeostasis / 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 / regulation of mitochondrial membrane potential / 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 Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Michel, M.A. / Scutts, S. / Komander, D. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Linkage and substrate specificity conferred by NZF ubiquitin binding domains Authors: Michel, M.A. / Scutts, S. / Komander, D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.6 KB | Display | ![]() |
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PDB format | ![]() | 199.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9b0bC ![]() 9b12C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 11017.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3316.815 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase #3: Protein | Mass: 17135.654 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.14 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→44.18 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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