+Open data
-Basic information
Entry | Database: PDB / ID: 8h4v | |||||||||
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Title | Mincle CRD complex with PGL trisaccharide | |||||||||
Components | C-type lectin domain family 4 member E | |||||||||
Keywords | SUGAR BINDING PROTEIN / Immune receptor / Innate immunity / C-type lectin receptor / Mycobacterium leprae | |||||||||
Function / homology | Function and homology information Dectin-2 family / T cell differentiation involved in immune response / antifungal innate immune response / glycolipid binding / Fc-gamma receptor signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding ...Dectin-2 family / T cell differentiation involved in immune response / antifungal innate immune response / glycolipid binding / Fc-gamma receptor signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding / defense response to bacterium / external side of plasma membrane / calcium ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Ishizuka, S. / Nagae, M. / Yamasaki, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acs Cent.Sci. / Year: 2023 Title: PGL-III, a Rare Intermediate of Mycobacterium leprae Phenolic Glycolipid Biosynthesis, Is a Potent Mincle Ligand. Authors: Ishizuka, S. / van Dijk, J.H.M. / Kawakita, T. / Miyamoto, Y. / Maeda, Y. / Goto, M. / Le Calvez, G. / Groot, L.M. / Witte, M.D. / Minnaard, A.J. / van der Marel, G.A. / Ato, M. / Nagae, M. ...Authors: Ishizuka, S. / van Dijk, J.H.M. / Kawakita, T. / Miyamoto, Y. / Maeda, Y. / Goto, M. / Le Calvez, G. / Groot, L.M. / Witte, M.D. / Minnaard, A.J. / van der Marel, G.A. / Ato, M. / Nagae, M. / Codee, J.D.C. / Yamasaki, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h4v.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h4v.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h4v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8h4v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8h4v_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 8h4v_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/8h4v ftp://data.pdbj.org/pub/pdb/validation_reports/h4/8h4v | HTTPS FTP |
-Related structure data
Related structure data | 8hb5C 4zrwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 17443.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: CLEC4E / Production host: Escherichia coli (E. coli) / References: UniProt: E1BHM0 #2: Polysaccharide | Type: oligosaccharide / Mass: 528.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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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: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M imidazole (pH 7.5), 0.2M sodium acetate trihydrate, 10%(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.36 Å / Num. obs: 14310 / % possible obs: 100 % / Redundancy: 40.2 % / Biso Wilson estimate: 76.34 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.021 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 42.6 % / Rmerge(I) obs: 4.059 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 14310 / CC1/2: 0.601 / Rpim(I) all: 0.627 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZRW Resolution: 2.4→42.35 Å / SU ML: 0.4518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.398 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.8191781502 Å / Origin y: 5.54886933536 Å / Origin z: -17.9022935827 Å
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Refinement TLS group | Selection details: all |