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Yorodumi- PDB-6z32: Human cation-independent mannose 6-phosphate/IGF2 receptor domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z32 | |||||||||||||||
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Title | Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11 | |||||||||||||||
Components | Cation-independent mannose-6-phosphate receptor | |||||||||||||||
Keywords | SUGAR BINDING PROTEIN / Cation-independent mannose 6-phosphate receptor / Insulin-like growth factor 2 receptor / Mannose 6-phosphate | |||||||||||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / 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 / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / 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: 3.47 Å | |||||||||||||||
Authors | Bochel, A.J. / Williams, C. / McCoy, A.J. / Hoppe, H. / Winter, A.J. / Nicholls, R.D. / Harlos, K. / Jones, Y.E. / Berger, I. / Hassan, B. / Crump, M.P. | |||||||||||||||
Funding support | United Kingdom, 4items
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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 | 6z32.cif.gz | 548.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z32.ent.gz | 456.6 KB | Display | PDB format |
PDBx/mmJSON format | 6z32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z32 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z32 | HTTPS FTP |
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-Related structure data
Related structure data | 6z30C 6z31C 1gp0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 934 - 1646 / Label seq-ID: 22 - 734
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-Components
#1: Protein | Mass: 80832.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ETGQLKHHHHHHEFTTTDTDQ are vector derived / Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P11717 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / | #4: Sugar | 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: 3.75 Å3/Da / Density % sol: 67.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 1.6 M MgSO4, 10 mM mannose 6-phosphate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.05811 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05811 Å / Relative weight: 1 |
Reflection | Resolution: 3.47→89.72 Å / Num. obs: 30224 / % possible obs: 98.55 % / Redundancy: 14.5 % / CC1/2: 0.997 / Net I/σ(I): 6.03 |
Reflection shell | Resolution: 3.47→3.59 Å / Redundancy: 14.9 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2944 / CC1/2: 0.127 / % possible all: 98.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology models of D7, 8, 9, 10, Crystal structure of D11 (1GP0) Resolution: 3.47→89.72 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.913 / SU B: 105.945 / SU ML: 0.706 / Cross valid method: THROUGHOUT / ESU R Free: 0.628 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 197.426 Å2
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Refinement step | Cycle: 1 / Resolution: 3.47→89.72 Å
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