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Yorodumi- PDB-6ino: Crystal structure of the CysR-CTLD2 fragment of human MR at acidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ino | |||||||||
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Title | Crystal structure of the CysR-CTLD2 fragment of human MR at acidic pH (pH 4.6) | |||||||||
Components | Macrophage mannose receptor 1 | |||||||||
Keywords | IMMUNE SYSTEM / CD206 / mannose receptor family / pH-dependent / conformational change / scavenger receptor | |||||||||
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: 3.054 Å | |||||||||
Authors | Hu, Z. / He, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Structural basis of the pH-dependent conformational change of the N-terminal region of human mannose receptor/CD206. Authors: Hu, Z. / Wang, Y. / Cheng, C. / He, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ino.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ino.ent.gz | 149.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ino.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ino_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 6ino_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 6ino_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 6ino_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/6ino ftp://data.pdbj.org/pub/pdb/validation_reports/in/6ino | HTTPS FTP |
-Related structure data
Related structure data | 6innC 6inuC 6invC 6ioeC 5xtsS S: Starting model for refinement 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: 54412.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MRC1, CLEC13D, CLEC13DL, MRC1L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22897 |
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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: 4.04 Å3/Da / Density % sol: 69.57 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 2.0 M sodium chloride, 0.1 M sodium acetate trihydrate (pH 4.6) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2018 |
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→30 Å / Num. obs: 32631 / % possible obs: 98.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 11.615 |
Reflection shell | Resolution: 3.05→3.16 Å / Rmerge(I) obs: 0.634 / Num. unique obs: 3217 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XTS Resolution: 3.054→29.755 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.054→29.755 Å
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Refine LS restraints |
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LS refinement shell |
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