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Yorodumi- PDB-6z31: Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z31 | ||||||||||||
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Title | Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8 | ||||||||||||
Components | Cation-independent mannose-6-phosphate receptor | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Mannose 6-phosphate / Cation-independent mannose 6-phosphate receptor / Insulin-like growth factor 2 receptor / P-type lectin | ||||||||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / Cargo recognition for clathrin-mediated endocytosis / late endosome / Clathrin-mediated endocytosis / signaling receptor activity / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||||||||
Authors | Bochel, A.J. / Williams, C. / Crump, M.P. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Structure / Year: 2020 Title: Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9. Authors: Bochel, A.J. / Williams, C. / McCoy, A.J. / Hoppe, H.J. / Winter, A.J. / Nicholls, R.D. / Harlos, K. / Jones, E.Y. / Berger, I. / Hassan, A.B. / Crump, M.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z31.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z31.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 6z31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z31 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z31 | 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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Unit cell |
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-Components
#1: Protein | Mass: 15082.927 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11717 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.12 Å3/Da / Density % sol: 60.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.5 M Ammonium sulphate, 0.1 M Tris pH 8.5, 12 % glycerol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→36.02 Å / Num. obs: 12121 / % possible obs: 98.98 % / Redundancy: 4.7 % / Biso Wilson estimate: 40.52 Å2 / CC1/2: 0.975 / Net I/σ(I): 5.59 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 1170 / CC1/2: 0.686 / % possible all: 95.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Domain 10 from the crystal structure of cation-independent mannose 6-phosphate receptor domains 9-10 (separate deposition) Resolution: 2.56→36.02 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→36.02 Å
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LS refinement shell | Resolution: 2.56→2.65 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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