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Yorodumi- PDB-9azj: Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 9azj | ||||||||||||
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Title | Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / ubiquitin binding domain / UBAN / NZF / NF-kB / NEMO | ||||||||||||
Function / homology | Function and homology information IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / protein linear polyubiquitination / IkappaB kinase complex / LUBAC complex / establishment of vesicle localization / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / transferrin receptor binding ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / protein linear polyubiquitination / IkappaB kinase complex / LUBAC complex / establishment of vesicle localization / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / transferrin receptor binding / positive regulation of xenophagy / IkBA variant leads to EDA-ID / CD40 receptor complex / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / negative regulation of necroptotic process / hypothalamus gonadotrophin-releasing hormone neuron development / anoikis / 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 / positive regulation of T cell receptor signaling pathway / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / neuron projection morphogenesis / canonical NF-kappaB signal transduction / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / signaling adaptor activity / ubiquitin ligase complex / 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 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å | ||||||||||||
Authors | Michel, M.A. / Scutts, S. / Komander, D. | ||||||||||||
Funding support | United Kingdom, Australia, European Union, 3items
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Citation | Journal: To be published Title: Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Authors: Michel, M.A. / Scutts, S. / Komander, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9azj.cif.gz | 280.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9azj.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 9azj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/9azj ftp://data.pdbj.org/pub/pdb/validation_reports/az/9azj | HTTPS FTP |
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-Related structure data
Related structure data | 9avtC 9avwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12643.395 Da / Num. of mol.: 4 / Mutation: K285C Source method: isolated from a genetically manipulated source Details: K285C mutation for chemical ubiquitination / Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K9 #2: Protein/peptide | Mass: 3245.738 Da / Num. of mol.: 2 / Fragment: HOIP NZF domain, residues 351-379 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 | Mass: 8622.922 Da / Num. of mol.: 3 / Mutation: G76C 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 | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.6 Details: 150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→55.81 Å / Num. obs: 15095 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 122.12 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.048 / Rrim(I) all: 0.115 / Net I/σ(I): 9.1 / Num. measured all: 84793 |
Reflection shell | Resolution: 3.32→3.59 Å / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.077 / Num. measured all: 17542 / Num. unique obs: 3039 / CC1/2: 0.688 / Rpim(I) all: 0.475 / Rrim(I) all: 1.18 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→50.72 Å / SU ML: 0.4796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6442 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: poorly ordered ubiquitin and HOIP NZF domain (chain E, F). NEMO chain A and chain B chemically ubiquitinated via a disulphide bond at NEMO K285C-Ub G76C.
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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: 167.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.32→50.72 Å
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Refine LS restraints |
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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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