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Yorodumi- PDB-3jsv: Crystal structure of mouse NEMO CoZi in complex with Lys63-linked... -
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-Basic information
Entry | Database: PDB / ID: 3jsv | ||||||
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Title | Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin | ||||||
Components |
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Keywords | SIGNALING PROTEIN/TRANSCRIPTION / ubiquitin / coiled-coil / cellular signaling / Cytoplasm / Isopeptide bond / Nucleus / Phosphoprotein / Ubl conjugation / Coiled coil / Disulfide bond / Metal-binding / Transcription / Transcription regulation / Zinc / Zinc-finger / SIGNALING PROTEIN-TRANSCRIPTION COMPLEX | ||||||
Function / homology | Function and homology information SUMOylation of immune response proteins / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / RIP-mediated NFkB activation via ZBP1 / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...SUMOylation of immune response proteins / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / RIP-mediated NFkB activation via ZBP1 / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IkappaB kinase complex / TRAF6 mediated NF-kB activation / Ovarian tumor domain proteases / PKR-mediated signaling / establishment of vesicle localization / linear polyubiquitin binding / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / : / : / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / transferrin receptor binding / protein modification process => GO:0036211 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Ub-specific processing proteases / peroxisome proliferator activated receptor binding / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of macroautophagy / B cell homeostasis / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / polyubiquitin modification-dependent protein binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / signaling adaptor activity / canonical NF-kappaB signal transduction / negative regulation of endoplasmic reticulum stress-induced intrinsic 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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 / cytosolic ribosome / Downregulation of TGF-beta receptor signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Yoshikawa, A. / Sato, Y. / Mimura, H. / Yamashita, M. / Yamagata, A. / Fukai, S. | ||||||
Citation | Journal: Febs Lett. / Year: 2009 Title: Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin Authors: Yoshikawa, A. / Sato, Y. / Yamashita, M. / Mimura, H. / Yamagata, A. / Fukai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jsv.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jsv.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/3jsv ftp://data.pdbj.org/pub/pdb/validation_reports/js/3jsv | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K63R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS | ||
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#2: Protein | Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: X77D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS | ||
#3: Protein | Mass: 11105.640 Da / Num. of mol.: 2 / Fragment: residues 250-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ikbkg, Nemo, NEMO(249-343) / Plasmid: pCold / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O88522 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 11492 / Num. obs: 11492 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 31 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.066 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.7→2.75 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.216 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.5 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 110720.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.6733 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→49.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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