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Yorodumi- PDB-5zuj: Binding and Enhanced Binding between Key Immunity Proteins TRAF6 ... -
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-Basic information
Entry | Database: PDB / ID: 5zuj | ||||||||||||
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Title | Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA | ||||||||||||
Components |
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Keywords | PROTEIN BINDING / Complex / TRAF6 / TIFA mutant peptide | ||||||||||||
Function / homology | Function and homology information protein kinase B binding / interleukin-17A-mediated signaling pathway / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex / positive regulation of lipopolysaccharide-mediated signaling pathway ...protein kinase B binding / interleukin-17A-mediated signaling pathway / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / 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 / regulation of canonical NF-kappaB signal transduction / MyD88-dependent toll-like receptor signaling pathway / ubiquitin-ubiquitin ligase activity / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / T-helper 1 type immune response / activation of protein kinase activity / cytoplasmic pattern recognition receptor signaling pathway / non-canonical NF-kappaB signal transduction / odontogenesis of dentin-containing tooth / protein K63-linked ubiquitination / cellular response to cytokine stimulus / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / antiviral innate immune response / TRAF6 mediated NF-kB activation / autophagosome assembly / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / protein autoubiquitination / positive regulation of T cell proliferation / positive regulation of JUN kinase activity / bone resorption / lipopolysaccharide-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / 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 / tumor necrosis factor-mediated signaling pathway / TICAM1,TRAF6-dependent induction of TAK1 complex / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-2 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / response to interleukin-1 / lipid droplet / ossification / 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 / positive regulation of protein ubiquitination / Regulation of NF-kappa B signaling / neural tube closure / activated TAK1 mediates p38 MAPK activation / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / protein homooligomerization / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / positive regulation of DNA-binding transcription factor activity / histone deacetylase binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of interleukin-6 production / antigen processing and presentation of exogenous peptide antigen via MHC class II / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Downstream TCR signaling / PIP3 activates AKT signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / cellular response to lipopolysaccharide Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Huang, W.C. / Maestre-Reyna, M. / Hsiao, T.C. / Tsai, M.D. | ||||||||||||
Funding support | Taiwan, 3items
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Citation | Journal: Chembiochem / Year: 2019 Title: Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA. Authors: Huang, W.C. / Liao, J.H. / Hsiao, T.C. / Wei, T.W. / Maestre-Reyna, M. / Bessho, Y. / Tsai, M.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zuj.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zuj.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/5zuj ftp://data.pdbj.org/pub/pdb/validation_reports/zu/5zuj | HTTPS FTP |
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-Related structure data
Related structure data | 6a33C 1lb5S 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: 18857.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6, RNF85 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y4K3, RING-type E3 ubiquitin transferase |
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#2: Protein/peptide | Mass: 1639.500 Da / Num. of mol.: 1 / Mutation: S174Q, M179D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CG3 |
#3: 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: 3.14 Å3/Da / Density % sol: 60.79 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 7.5 Details: 0.1 M HEPES sodium, pH 7.5, 1M Sodium citrate tribasic dihydrate, 10 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 19, 2017 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.62 Å / Num. obs: 9019 / % possible obs: 99.81 % / Redundancy: 1.96 % / Biso Wilson estimate: 49.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05055 / Rpim(I) all: 0.05055 / Rrim(I) all: 0.07149 / Net I/σ(I): 10.57 |
Reflection shell | Resolution: 2.6→2.693 Å / Rmerge(I) obs: 0.4142 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 863 / CC1/2: 0.777 / Rpim(I) all: 0.4142 / Rrim(I) all: 0.5858 / % possible all: 99.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LB5 Resolution: 2.6→44.616 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.2 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→44.616 Å
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Refine LS restraints |
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LS refinement shell |
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