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Yorodumi- PDB-4owf: Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 4owf | |||||||||
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Title | Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain | |||||||||
Components |
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Keywords | TRANSCRIPTION/PROTEIN BINDING / LUBAC / NF-kappa B / NEMO / HOIP / TRANSCRIPTION-PROTEIN BINDING complex | |||||||||
Function / homology | Function and homology information 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 / SUMOylation of immune response proteins / protein linear polyubiquitination / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling ...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 / SUMOylation of immune response proteins / protein linear polyubiquitination / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IkappaB kinase complex / LUBAC complex / TRAF6 mediated NF-kB activation / Ovarian tumor domain proteases / PKR-mediated signaling / establishment of vesicle localization / linear polyubiquitin binding / CD40 signaling pathway / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / RBR-type E3 ubiquitin transferase / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / positive regulation of xenophagy / transferrin receptor binding / activated TAK1 mediates p38 MAPK activation / CD40 receptor complex / NOD1/2 Signaling Pathway / Ub-specific processing proteases / negative regulation of necroptotic process / anoikis / K48-linked polyubiquitin modification-dependent protein binding / peroxisome proliferator activated receptor binding / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / B cell homeostasis / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / signaling adaptor activity / ubiquitin ligase complex / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / mitotic spindle / spindle pole / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / protein heterodimerization activity / protein domain specific binding / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Rahighi, S. / Fujita, H. / Kawasaki, M. / Kato, R. / Iwai, K. / Wakatsuki, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Mol.Cell.Biol. / Year: 2014 Title: Mechanism Underlying I kappa B Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex. Authors: Fujita, H. / Rahighi, S. / Akita, M. / Kato, R. / Sasaki, Y. / Wakatsuki, S. / Iwai, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4owf.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4owf.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 4owf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/4owf ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4owf | HTTPS FTP |
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-Related 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: 10648.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ikbkg,Nemo / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O88522, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | | Mass: 3316.815 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31,ZIBRA / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #3: Chemical | ChemComp-ZN / | #4: 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: 2.92 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Co-crystals were obtained after 6 days in 20% (w/v) PEG-3350 and 0.2 M DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.28254 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28254 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.96 Å / Num. all: 120482 / Num. obs: 15849 / % possible obs: 83.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.1 / % possible all: 66.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY . 3FX0 AND 2WX0 Resolution: 2→32.96 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.846 / SU B: 4.726 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.252 Å2
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Refinement step | Cycle: 1 / Resolution: 2→32.96 Å
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