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Open data
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Basic information
Entry | Database: PDB / ID: 2bpe | ||||||
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Title | STRUCTURE OF MURINE DECTIN-1 | ||||||
![]() | DECTIN-1 | ||||||
![]() | RECEPTOR / DECTIN-1 / BETA-GLUCAN / FUNGAL RECOGNITION / C-TYPE LECTIN-LIKE DOMAIN / CTLD | ||||||
Function / homology | ![]() (1->3)-beta-D-glucan immune receptor activity / detection of yeast / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production / cell surface pattern recognition receptor signaling pathway / antifungal innate immune response / opsonin binding ...(1->3)-beta-D-glucan immune receptor activity / detection of yeast / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production / cell surface pattern recognition receptor signaling pathway / antifungal innate immune response / opsonin binding / positive regulation of interleukin-23 production / positive regulation of cytokine production involved in immune response / CLEC7A (Dectin-1) signaling / response to yeast / leukocyte activation involved in immune response / positive regulation of stress-activated MAPK cascade / cell activation / phagocytosis, recognition / cellular response to molecule of fungal origin / positive regulation of T-helper 17 type immune response / regulation of canonical NF-kappaB signal transduction / pattern recognition receptor activity / polysaccharide binding / phagocytosis, engulfment / stimulatory C-type lectin receptor signaling pathway / positive regulation of interleukin-10 production / positive regulation of phagocytosis / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / cell-cell adhesion / positive regulation of DNA-binding transcription factor activity / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / inflammatory response / external side of plasma membrane / innate immune response / cell surface / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brown, J. / O'Callaghan, C.A. / Marshall, A.S.J. / Gilbert, R.J.C. / Siebold, C. / Gordon, S. / Brown, G.D. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structure of the Fungal Beta-Glucan-Binding Immune Receptor Dectin-1: Implications for Function. Authors: Brown, J. / O'Callaghan, C.A. / Marshall, A.S.J. / Gilbert, R.J.C. / Siebold, C. / Gordon, S. / Brown, G.D. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.3 KB | Display | ![]() |
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PDB format | ![]() | 53.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bpdSC ![]() 2bphC ![]() 2cl8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper: (Code: given Matrix: (-1, 0.00063, 0.001), Vector: |
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Components
#1: Protein | Mass: 16227.040 Da / Num. of mol.: 2 Fragment: EXTRACELLULAR BETA-GLUCAN RECOGNITION DOMAIN RESIDUES 113-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.36 % Description: IN ADDITION TO THIS MODEL, CASPR GENERATED HOMOLOGY MODELS AND TRUNCATED MODELS TO USE IN MOLECULAR REPLACEMENT SEARCH |
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Crystal grow | pH: 4.6 Details: 2M SODIUM CHLORIDE, 0.1M SODIUM ACETATE PH4.6, pH 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 11, 2004 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 22768 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / % possible all: 76.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BPD Resolution: 2.25→73.32 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.791 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→73.32 Å
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Refine LS restraints |
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