+Open data
-Basic information
Entry | Database: PDB / ID: 1fyx | ||||||
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Title | CRYSTAL STRUCTURE OF P681H MUTANT OF TIR DOMAIN OF HUMAN TLR2 | ||||||
Components | TOLL-LIKE RECEPTOR 2 | ||||||
Keywords | SIGNALING PROTEIN / beta-alpha-beta fold | ||||||
Function / homology | Function and homology information toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide ...toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / negative regulation of synapse assembly / lipopolysaccharide immune receptor activity / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / positive regulation of matrix metallopeptidase secretion / toll-like receptor 2 signaling pathway / I-kappaB phosphorylation / positive regulation of interleukin-18 production / Toll-like receptor binding / central nervous system myelin formation / leukotriene metabolic process / Regulation of TLR by endogenous ligand / response to fatty acid / peptidoglycan binding / NAD+ nucleotidase, cyclic ADP-ribose generating / microglia development / MyD88 deficiency (TLR2/4) / negative regulation of phagocytosis / IRAK4 deficiency (TLR2/4) / pattern recognition receptor activity / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / nitric oxide metabolic process / positive regulation of oligodendrocyte differentiation / RSV-host interactions / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / learning / positive regulation of interleukin-8 production / cell projection / response to progesterone / lipopolysaccharide binding / microglial cell activation / response to insulin / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity / response to toxic substance / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / ER-Phagosome pathway / cell body / defense response to virus / receptor complex / response to hypoxia / defense response to Gram-positive bacterium / inflammatory response / membrane raft / immune response / negative regulation of cell population proliferation / innate immune response / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Xu, Y. / Tao, X. / Shen, B. / Horng, T. / Medzhitov, R. / Manley, J.L. / Tong, L. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Structural basis for signal transduction by the Toll/interleukin-1 receptor domains. Authors: Xu, Y. / Tao, X. / Shen, B. / Horng, T. / Medzhitov, R. / Manley, J.L. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fyx.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyx.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fyx_validation.pdf.gz | 368.2 KB | Display | wwPDB validaton report |
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Full document | 1fyx_full_validation.pdf.gz | 371.9 KB | Display | |
Data in XML | 1fyx_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 1fyx_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyx ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18355.545 Da / Num. of mol.: 1 / Fragment: TIR DOMAIN / Mutation: P681H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O60603 |
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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: 5.4 Å3/Da / Density % sol: 77.22 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 100 mM cacodylate, 10 % PEG 8000, 20 % DMSO, 200 mM MgCl2, 5 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 32-ID / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 16, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. all: 10500 / Num. obs: 10002 / % possible obs: 96 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.232 / % possible all: 68 |
-Processing
Software |
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Refinement | Resolution: 2.8→20 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 7.5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |