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Yorodumi- PDB-7nuw: Crystal structure of the TIR domain of human TLR1 (crystallised w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nuw | ||||||
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Title | Crystal structure of the TIR domain of human TLR1 (crystallised with Zn2+ ions) | ||||||
Components | Toll-like receptor 1 | ||||||
Keywords | SIGNALING PROTEIN / TOLL-LIKE RECEPTOR / TIR DOMAIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Vakhrameev, D.D. / Luginina, A.P. / Shevtsov, M.B. / Lushpa, V.A. / Mineev, K.S. / Borshchevskiy, V.I. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn 2+ ions. Authors: Lushpa, V.A. / Goncharuk, M.V. / Lin, C. / Zalevsky, A.O. / Talyzina, I.A. / Luginina, A.P. / Vakhrameev, D.D. / Shevtsov, M.B. / Goncharuk, S.A. / Arseniev, A.S. / Borshchevskiy, V.I. / Wang, X. / Mineev, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nuw.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nuw.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 7nuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/7nuw ftp://data.pdbj.org/pub/pdb/validation_reports/nu/7nuw | HTTPS FTP |
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-Related structure data
Related structure data | 7nt7C 7nuxC 1fyvS S: Starting model for refinement C: citing same article (ref.) |
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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: 19074.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TLR1, KIAA0012 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS References: UniProt: Q15399, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase |
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#2: 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: 2.68 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.6 Details: 170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton) + Zinc chloride(molar ratio zinc ...Details: 170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton) + Zinc chloride(molar ratio zinc chloride:protein 1:1). Growth at +4 for 3-4 months. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.96 Å / Num. obs: 17010 / % possible obs: 99.73 % / Redundancy: 38.2 % / Biso Wilson estimate: 46.03 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.0169 / Net I/σ(I): 22.88 |
Reflection shell | Resolution: 1.9→1.968 Å / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1664 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.8749 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FYV Resolution: 1.9→43.96 Å / SU ML: 0.2877 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4796 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.34 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å
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