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Yorodumi- PDB-3hct: Crystal structure of TRAF6 in complex with Ubc13 in the P1 space group -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hct | ||||||
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Title | Crystal structure of TRAF6 in complex with Ubc13 in the P1 space group | ||||||
Components |
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Keywords | SIGNALING PROTEIN/LIGASE / cross-brace / beta-beta-alpha / Coiled coil / Cytoplasm / Metal-binding / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger / ATP-binding / DNA damage / DNA repair / Isopeptide bond / Ligase / Nucleotide-binding / SIGNALING PROTEIN-LIGASE COMPLEX | ||||||
Function / homology | Function and homology information : / UBC13-UEV1A complex / UBC13-MMS2 complex / tumor necrosis factor receptor superfamily binding / ubiquitin conjugating enzyme complex / protein kinase B binding / interleukin-17A-mediated signaling pathway / ubiquitin-protein transferase activator activity / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation ...: / UBC13-UEV1A complex / UBC13-MMS2 complex / tumor necrosis factor receptor superfamily binding / ubiquitin conjugating enzyme complex / protein kinase B binding / interleukin-17A-mediated signaling pathway / ubiquitin-protein transferase activator activity / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / DNA double-strand break processing / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / positive regulation of protein K63-linked ubiquitination / toll-like receptor 3 signaling pathway / CD40 receptor complex / positive regulation of lipopolysaccharide-mediated signaling pathway / myeloid dendritic cell differentiation / TRIF-dependent toll-like receptor signaling pathway / Regulated proteolysis of p75NTR / activation of NF-kappaB-inducing kinase activity / positive regulation of transcription regulatory region DNA binding / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / ubiquitin conjugating enzyme binding / regulation of immunoglobulin production / postreplication repair / regulation of canonical NF-kappaB signal transduction / positive regulation of double-strand break repair / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / positive regulation of intracellular signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / T-helper 1 type immune response / cytoplasmic pattern recognition receptor signaling pathway / ubiquitin conjugating enzyme activity / activation of protein kinase activity / cellular response to cytokine stimulus / odontogenesis of dentin-containing tooth / protein K63-linked ubiquitination / non-canonical NF-kappaB signal transduction / Fc-epsilon receptor signaling pathway / antiviral innate immune response / stimulatory C-type lectin receptor signaling pathway / TRAF6 mediated NF-kB activation / autophagosome assembly / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / regulation of DNA repair / protein autoubiquitination / ubiquitin ligase complex / positive regulation of JUN kinase activity / bone resorption / lipopolysaccharide-mediated signaling pathway / negative regulation of TORC1 signaling / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of T cell proliferation / TICAM1,TRAF6-dependent induction of TAK1 complex / positive regulation of DNA repair / tumor necrosis factor-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-2 production / extrinsic component of cytoplasmic side of plasma membrane / TRAF6-mediated induction of TAK1 complex within TLR4 complex / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / lipid droplet / ossification / response to interleukin-1 / TICAM1, RIP1-mediated IKK complex recruitment / osteoclast differentiation / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / positive regulation of protein ubiquitination / Regulation of NF-kappa B signaling / neural tube closure / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Yin, Q. / Lin, S.-C. / Lamothe, B. / Lu, M. / Lo, Y.-C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. ...Yin, Q. / Lin, S.-C. / Lamothe, B. / Lu, M. / Lo, Y.-C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. / Lenardo, M.J. / Darnay, B.G. / Wu, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: E2 interaction and dimerization in the crystal structure of TRAF6. Authors: Yin, Q. / Lin, S.C. / Lamothe, B. / Lu, M. / Lo, Y.C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. / Lenardo, M.J. / Darnay, B.G. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hct.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hct.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hct ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hct | HTTPS FTP |
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-Related structure data
Related structure data | 3hcsSC 3hcuC 2gmiS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13775.906 Da / Num. of mol.: 1 / Fragment: RING and Zinc Finger 1: UNP residues 50-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF85, TRAF6 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus RIPL / References: UniProt: Q9Y4K3 | ||
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#2: Protein | Mass: 17440.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus RIPL / References: UniProt: P61088, ubiquitin-protein ligase | ||
#3: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 8% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 14, 2007 / Details: Mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.06→30 Å / Num. obs: 16146 / % possible obs: 91.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.037 / Χ2: 3.715 / Net I/σ(I): 39.692 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2GMI, 3HCS Resolution: 2.1→30 Å / Occupancy max: 1.17 / Occupancy min: 0.93 / σ(F): 0
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Solvent computation | Bsol: 79.746 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.66 Å2 / Biso mean: 41.53 Å2 / Biso min: 17.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Xplor file |
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