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Yorodumi- PDB-7jud: C-type carbohydrate-recognition domain 4 of the mannose receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jud | ||||||
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Title | C-type carbohydrate-recognition domain 4 of the mannose receptor complexed with methyl-mannoside | ||||||
Components | Macrophage mannose receptor 1 | ||||||
Keywords | SUGAR BINDING PROTEIN / GLYCOBIOLOGY / CARBOHYDRATE-BINDING PROTEIN / C-TYPE LECTIN / COMPLEX | ||||||
Function / homology | Function and homology information cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Weis, W.I. / Feinberg, H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206. Authors: Feinberg, H. / Jegouzo, S.A.F. / Lasanajak, Y. / Smith, D.F. / Drickamer, K. / Weis, W.I. / Taylor, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jud.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jud.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 7jud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jud_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7jud_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7jud_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7jud_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/7jud ftp://data.pdbj.org/pub/pdb/validation_reports/ju/7jud | HTTPS FTP |
-Related structure data
Related structure data | 7jubC 7jucC 7jueC 7jufC 7jugC 7juhC 7l61C 7l62C 7l63C 7l64C 7l65C 7l66C 7l67C 7l68C C: citing same article (ref.) |
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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: 15493.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MRC1, CLEC13D, CLEC13DL, MRC1L1 / Plasmid: pT5T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22897 #2: Chemical | #3: Sugar | #4: Water | ChemComp-HOH / | 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: 1.92 Å3/Da / Density % sol: 35.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Protein solution: 6.0mg/ml protein in 5mM CaCl2, 10mM Tris, pH 8.0, 25mM NaCl, and 50mM Me-Man Reservoir solution: 2.5% Peg 3.35K or 10% Peg 400, 0.1M Mes pH=6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→36.28 Å / Num. obs: 44495 / % possible obs: 97.2 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.043 / Rrim(I) all: 0.118 / Net I/σ(I): 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IEGG Resolution: 1.4→31.93 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 17.99 / 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: 61.39 Å2 / Biso mean: 19.1528 Å2 / Biso min: 7.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→31.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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