+Open data
-Basic information
Entry | Database: PDB / ID: 1lb6 | ||||||
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Title | TRAF6-CD40 Complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / TRAF6-CD40 complex | ||||||
Function / homology | Function and homology information CD154 receptor binding / cellular response to erythropoietin / response to peptide / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / protein kinase B binding / interleukin-17A-mediated signaling pathway / varicosity ...CD154 receptor binding / cellular response to erythropoietin / response to peptide / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / protein kinase B binding / interleukin-17A-mediated signaling pathway / varicosity / 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 / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / positive regulation of isotype switching to IgG isotypes / 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 / positive regulation of endothelial cell apoptotic process / 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 / B cell activation / response to cobalamin / activation of protein kinase activity / cytoplasmic pattern recognition receptor signaling pathway / B cell proliferation / response to type II interferon / defense response to protozoan / 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 / positive regulation of blood vessel endothelial cell migration / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / protein autoubiquitination / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of JUN kinase activity / positive regulation of tyrosine phosphorylation of STAT protein / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein ubiquitination / Regulation of NF-kappa B signaling / antigen binding / neural tube closure / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / positive regulation of MAP kinase activity / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / cytoplasmic side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O. / Vologodskaia, M. / Yim, M. ...Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O. / Vologodskaia, M. / Yim, M. / Du, K. / Singh, S. / Pike, J.W. / Darnay, B.G. / Choi, Y. / Wu, H. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Distinct molecular mechanism for initiating TRAF6 signalling. Authors: Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O.K. / Vologodskaia, M. / Yim, M. / Du, K. / Singh, S. / Pike, J.W. / Darnay, B.G. / Choi, Y. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lb6.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lb6.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/1lb6 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/1lb6 | 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: 18676.549 Da / Num. of mol.: 1 / Fragment: residues 347-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4K3 |
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#2: Protein/peptide | Mass: 1134.214 Da / Num. of mol.: 1 / Fragment: residues 230-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD40 / Production host: Escherichia coli (E. coli) / References: UniProt: P25942 |
#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: 2.24 Å3/Da / Density % sol: 44.97 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→33.2 Å / Num. obs: 15569 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 9.7 Å2 |
Reflection shell | Resolution: 1.8→1.91 Å / Num. unique all: 1887 / % possible all: 66.9 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 40 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 93 % / Rmerge(I) obs: 0.221 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TRAF6 apo form Resolution: 1.8→33.16 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.3 Å2 | |||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→33.16 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.203 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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