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Yorodumi- PDB-3b0a: Crystal structure of the mouse HOIL1-L-NZF in complex with linear... -
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-Basic information
Entry | Database: PDB / ID: 3b0a | ||||||
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Title | Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin | ||||||
Components |
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Keywords | SIGNALING PROTEIN/METAL BINDING PROTEIN / protein complex / SIGNALING PROTEIN-METAL BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information TNFR1-induced proapoptotic signaling / protein linear polyubiquitination / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / LUBAC complex / cytoplasmic sequestering of protein / RBR-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process ...TNFR1-induced proapoptotic signaling / protein linear polyubiquitination / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / LUBAC complex / cytoplasmic sequestering of protein / RBR-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / tumor necrosis factor-mediated signaling pathway / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein sequestering activity / 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 / protein kinase C binding / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex Authors: Sato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b0a.cif.gz | 188.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b0a.ent.gz | 150.3 KB | Display | PDB format |
PDBx/mmJSON format | 3b0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/3b0a ftp://data.pdbj.org/pub/pdb/validation_reports/b0/3b0a | HTTPS FTP |
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-Related structure data
Related structure data | 3b08SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17135.654 Da / Num. of mol.: 2 / Fragment: linear di ubiquitin, UNP residues 1-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG48 #2: Protein | Mass: 7277.155 Da / Num. of mol.: 2 / Fragment: UNP residues 192-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbck1, Rbck, Ubce7ip3, Uip28 / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9WUB0 #3: Chemical | ChemComp-TAM / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.89 Å3/Da / Density % sol: 57.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.45M tri-ammonium citrate (pH 7.0), 3% 1,6-diaminohexane, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2826 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2826 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 43879 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.9→1.92 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.85 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B08 Resolution: 1.9→45.438 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.48 / σ(F): 2.12 / Phase error: 23.17 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.179 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.24 Å2 / Biso mean: 39.4892 Å2 / Biso min: 17.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45.438 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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