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Yorodumi- PDB-1q8m: Crystal structure of the human myeloid cell activating receptor TREM-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q8m | ||||||
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Title | Crystal structure of the human myeloid cell activating receptor TREM-1 | ||||||
Components | triggering receptor expressed on myeloid cells 1TREM1 | ||||||
Keywords | IMMUNE SYSTEM RECEPTOR / V-type Ig-like domain / Immunoglobulin-like | ||||||
Function / homology | Function and homology information receptor decoy activity / neutrophil-mediated killing of gram-negative bacterium / humoral immune response / neutrophil chemotaxis / DAP12 interactions / Cell surface interactions at the vascular wall / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / scaffold protein binding ...receptor decoy activity / neutrophil-mediated killing of gram-negative bacterium / humoral immune response / neutrophil chemotaxis / DAP12 interactions / Cell surface interactions at the vascular wall / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / scaffold protein binding / adaptive immune response / intracellular signal transduction / innate immune response / cell surface / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Radaev, S. / Kattah, M. / Rostro, B. / Colonna, M. / Sun, P.D. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Crystal structure of the human myeloid cell activating receptor TREM-1 Authors: Radaev, S. / Kattah, M. / Rostro, B. / Colonna, M. / Sun, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q8m.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8m.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 1q8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8m ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8m | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 14952.163 Da / Num. of mol.: 4 / Fragment: Extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TREM1 / Plasmid: Pet-22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP99 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GSH / | #4: Water | ChemComp-HOH / | |
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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: 3.3 Å3/Da / Density % sol: 62.76 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: Ammonium sulfate, MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5.7 / PH range high: 5.4 | ||||||||||||||||||||||||
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: 19-ID / Wavelength: 1.0376, 0.9641, 0.9790, 0.9791 | |||||||||||||||
Detector | Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→46 Å / Num. all: 52139 / Num. obs: 52139 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.086 / Net I/σ(I): 23.5 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 2369 / Rsym value: 0.44 / % possible all: 95.9 | |||||||||||||||
Reflection | *PLUS Num. obs: 23897 / % possible obs: 98.6 % / Rmerge(I) obs: 0.086 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.7 % / Num. unique obs: 2369 / Rmerge(I) obs: 0.44 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→46 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å /
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Refinement | *PLUS Lowest resolution: 46 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |