+Open data
-Basic information
Entry | Database: PDB / ID: 1fyv | ||||||
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Title | CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1 | ||||||
Components | TOLL-LIKE RECEPTOR 1 | ||||||
Keywords | SIGNALING PROTEIN / beta-alpha-beta fold parallel beta sheet | ||||||
Function / homology | Function and homology information Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / Toll-like receptor 2 binding / macrophage activation / Regulation of TLR by endogenous ligand / lipopeptide binding ...Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / Toll-like receptor 2 binding / macrophage activation / Regulation of TLR by endogenous ligand / lipopeptide binding / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / positive regulation of interleukin-6 production / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / ER-Phagosome pathway / receptor complex / immune response / inflammatory response / membrane raft / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / signal transduction / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 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 | 1fyv.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyv.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyv ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyv | 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: 19081.670 Da / Num. of mol.: 1 / Fragment: TIR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15399 |
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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: 5.35 Å3/Da / Density % sol: 77.02 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, 1.2M NaH2PO4/K2HPO4 5 mM DTT, 20% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→40 Å / Num. all: 9700 / Num. obs: 9374 / % possible obs: 97 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 40 | |||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.17 / % possible all: 91 |
-Processing
Software |
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Refinement | Resolution: 2.9→20 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 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 |