+Open data
-Basic information
Entry | Database: PDB / ID: 3whd | ||||||
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Title | C-type lectin, human MCL | ||||||
Components | C-type lectin domain family 4 member D | ||||||
Keywords | IMMUNE SYSTEM / c-type lectin / carbohydrate recognition / glycolipid binding / Plasmamembrane | ||||||
Function / homology | Function and homology information positive regulation of myeloid dendritic cell activation / T cell differentiation involved in immune response / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / Dectin-2 family / immunoglobulin receptor binding / D-mannose binding / tertiary granule membrane / ficolin-1-rich granule membrane ...positive regulation of myeloid dendritic cell activation / T cell differentiation involved in immune response / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / Dectin-2 family / immunoglobulin receptor binding / D-mannose binding / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / carbohydrate binding / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / defense response to bacterium / external side of plasma membrane / Neutrophil degranulation / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Furukawa, A. / Kamishikiryo, J. / Mori, D. / Toyonaga, K. / Okabe, Y. / Toji, A. / Kanda, R. / Miyake, Y. / Ose, T. / Yamasaki, S. / Maenaka, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL Authors: Furukawa, A. / Kamishikiryo, J. / Mori, D. / Toyonaga, K. / Okabe, Y. / Toji, A. / Kanda, R. / Miyake, Y. / Ose, T. / Yamasaki, S. / Maenaka, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3whd.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3whd.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 3whd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/3whd ftp://data.pdbj.org/pub/pdb/validation_reports/wh/3whd | HTTPS FTP |
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-Related 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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Unit cell |
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-Components
#1: Protein | Mass: 18266.561 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 61-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4D / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q8WXI8 #2: Chemical | #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: 2.93 Å3/Da / Density % sol: 58.09 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Apr 12, 2011 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→40.483 Å / Num. obs: 19569 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→40.483 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8372 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 22.62 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.18 Å2 / Biso mean: 34.8584 Å2 / Biso min: 18.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→40.483 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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