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Yorodumi- PDB-5b1w: Crystal structure of human dendritic cell inhibitory receptor (DC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b1w | |||||||||
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Title | Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form | |||||||||
Components | C-type lectin domain family 4 member A | |||||||||
Keywords | CARBOHYDRATE BINDING PROTEIN / C-type lectin domain / innate immunity / carbohydrate recognition | |||||||||
Function / homology | Function and homology information plasmacytoid dendritic cell antigen processing and presentation / antifungal innate immune response / negative regulation of cytokine production / CD8-positive, alpha-beta T cell activation / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / D-mannose binding / negative regulation of tumor necrosis factor production / transmembrane signaling receptor activity / carbohydrate binding ...plasmacytoid dendritic cell antigen processing and presentation / antifungal innate immune response / negative regulation of cytokine production / CD8-positive, alpha-beta T cell activation / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / D-mannose binding / negative regulation of tumor necrosis factor production / transmembrane signaling receptor activity / carbohydrate binding / adaptive immune response / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / calcium ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | |||||||||
Authors | Nagae, M. / Yamaguchi, Y. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Febs Lett. / Year: 2016 Title: Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan Authors: Nagae, M. / Ikeda, A. / Hanashima, S. / Kojima, T. / Matsumoto, N. / Yamamoto, K. / Yamaguchi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b1w.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b1w.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b1w_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 5b1w_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 5b1w_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 5b1w_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b1w ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b1w | HTTPS FTP |
-Related structure data
Related structure data | 5b1xC 3vykS C: citing same article (ref.) S: Starting model for refinement |
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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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15812.479 Da / Num. of mol.: 4 / Fragment: UNP residues 106-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4A, CLECSF6, DCIR, LLIR, HDCGC13P / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9UMR7 #2: Chemical | ChemComp-CA / #3: 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: 2.8 Å3/Da / Density % sol: 56.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-HCl (pH 8.5), 0.2M sodium acetate and 30%(w/v) polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→100 Å / Num. obs: 14032 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rsym value: 0.173 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VYK Resolution: 3.05→47.019 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→47.019 Å
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Refine LS restraints |
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LS refinement shell |
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