+Open data
-Basic information
Entry | Database: PDB / ID: 4fz5 | ||||||
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Title | Crystal Structure of Human TIRAP TIR-domain | ||||||
Components | Toll/interleukin-1 receptor domain-containing adapter protein | ||||||
Keywords | IMMUNE SYSTEM / TIRAP / Scaffold / MyD88 | ||||||
Function / homology | Function and homology information positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / myeloid cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of neutrophil chemotaxis / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / regulation of innate immune response / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / 3'-UTR-mediated mRNA stabilization / regulation of stress-activated MAPK cascade / cellular response to lipoteichoic acid / endocytic vesicle / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of B cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-12 production / protein kinase C binding / positive regulation of interleukin-8 production / positive regulation of protein-containing complex assembly / positive regulation of JNK cascade / ruffle membrane / positive regulation of interleukin-6 production / protein-macromolecule adaptor activity / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / molecular adaptor activity / defense response to Gram-positive bacterium / inflammatory response / innate immune response / cell surface / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Woo, J.R. / Kim, S. / Shoelson, S.E. / Park, S. | ||||||
Citation | Journal: Bull.Korean Chem.Soc. / Year: 2013 Title: X-ray Crystallographic Structure of TIR-Domain from the Human TIR-Domain Containing Adaptor Protein/MyD88 Adaptor-Like Protein (TIRAP/MAL) Authors: Woo, J.R. / Kim, S. / Shoelson, S.E. / Park, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fz5.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fz5.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/4fz5 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/4fz5 | HTTPS FTP |
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-Related structure data
Related structure data | 2y92S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16829.033 Da / Num. of mol.: 2 / Fragment: TIR domain, UNP residues 72-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIRAP, MAL / Production host: Escherichia coli (E. coli) / References: UniProt: P58753 |
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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: 2.95 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8.5 Details: 5%(v/v) PEG200, 0.1M TRIS, pH8.5, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 4941 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y92 Resolution: 3.6→50 Å
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Refinement step | Cycle: LAST / Resolution: 3.6→50 Å
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Refine LS restraints |
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