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Yorodumi- PDB-5gjg: Crystal structure of human TAK1/TAB1 fusion protein in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gjg | ||||||
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Title | Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 4 | ||||||
Components | TAK1 kinase - TAB1 chimera fusion protein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase-Transferase inhibitor complex / TAK1-TAB1 kinase | ||||||
Function / homology | Function and homology information positive regulation of cGAS/STING signaling pathway / histone kinase activity / MAP kinase kinase kinase kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / linear polyubiquitin binding / interleukin-17A-mediated signaling pathway / cardiac septum development / I-kappaB phosphorylation / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway ...positive regulation of cGAS/STING signaling pathway / histone kinase activity / MAP kinase kinase kinase kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / linear polyubiquitin binding / interleukin-17A-mediated signaling pathway / cardiac septum development / I-kappaB phosphorylation / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / type II transforming growth factor beta receptor binding / TRIF-dependent toll-like receptor signaling pathway / activation of NF-kappaB-inducing kinase activity / coronary vasculature development / ATAC complex / positive regulation of vascular associated smooth muscle cell migration / cellular response to angiotensin / anoikis / aorta development / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / toll-like receptor 4 signaling pathway / protein serine/threonine kinase binding / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / cytoplasmic pattern recognition receptor signaling pathway / p38MAPK cascade / non-canonical NF-kappaB signal transduction / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / positive regulation of macroautophagy / positive regulation of cell size / MAP kinase kinase kinase activity / MAP kinase activity / canonical NF-kappaB signal transduction / enzyme activator activity / positive regulation of cell cycle / stress-activated MAPK cascade / heart morphogenesis / positive regulation of JUN kinase activity / JNK cascade / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / positive regulation of interleukin-2 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / lung development / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / receptor tyrosine kinase binding / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / transcription coactivator binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / MAPK cascade / Downstream TCR signaling / Ca2+ pathway / cellular response to tumor necrosis factor / T cell receptor signaling pathway / cellular response to hypoxia / scaffold protein binding / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / nuclear speck / defense response to bacterium / inflammatory response / immune response / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / magnesium ion binding / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å | ||||||
Authors | Irie, M. / Nakamura, M. / Fukami, T.A. / Matsuura, T. / Morishima, K. | ||||||
Citation | Journal: Chem.Pharm.Bull. / Year: 2016 Title: Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD) Authors: Muraoka, T. / Ide, M. / Irie, M. / Morikami, K. / Miura, T. / Nishihara, M. / Kashiwagi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gjg.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gjg.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/5gjg ftp://data.pdbj.org/pub/pdb/validation_reports/gj/5gjg | HTTPS FTP |
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-Related structure data
Related structure data | 5gjdC 5gjfC 2evaS C: citing same article (ref.) S: Starting model for refinement |
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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: 35530.953 Da / Num. of mol.: 1 / Fragment: UNP residues 31-303,UNP residues 468-504 Source method: isolated from a genetically manipulated source Details: fusion of Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K7, TAK1, TAB1, MAP3K7IP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O43318, UniProt: Q15750, mitogen-activated protein kinase kinase kinase |
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#2: Chemical | ChemComp-6V5 / |
#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: 3.99 Å3/Da / Density % sol: 69.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.61→41.93 Å / Num. all: 17613 / Num. obs: 17613 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Rsym value: 0.094 / Net I/av σ(I): 7.732 / Net I/σ(I): 18.7 / Num. measured all: 126645 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2EVA Resolution: 2.61→41.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.605 / SU ML: 0.173 / SU R Cruickshank DPI: 0.2662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.218 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.36 Å2 / Biso mean: 59.236 Å2 / Biso min: 25.36 Å2
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Refinement step | Cycle: final / Resolution: 2.61→41.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.678 Å / Total num. of bins used: 20
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