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Yorodumi- PDB-6z30: Human cation-independent mannose 6-phosphate/ IGF2 receptor domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z30 | ||||||||||||
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Title | Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10 | ||||||||||||
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 / secretory granule membrane / post-embryonic development / trans-Golgi network membrane / liver development / clathrin-coated endocytic vesicle membrane / phosphoprotein binding / trans-Golgi network / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / late endosome / signaling receptor activity / spermatogenesis / endosome / endosome membrane / early endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 6z30.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z30.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 6z30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z30_validation.pdf.gz | 768.4 KB | Display | wwPDB validaton report |
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Full document | 6z30_full_validation.pdf.gz | 768.5 KB | Display | |
Data in XML | 6z30_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6z30_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z30 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z30 | HTTPS FTP |
-Related structure data
Related structure data | 6z31C 6z32C 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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Unit cell |
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-Components
#1: Protein | Mass: 33646.758 Da / Num. of mol.: 1 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 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M SPG buffer (succinic acid, sodium dihydrogen phosphate monohydrate, glycine) pH 9, 25 % PEG 1500 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.46 Å / Num. obs: 48880 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 21.15 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.12 |
Reflection shell | Resolution: 1.5→1.81 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3040 / CC1/2: 0.744 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology models Resolution: 1.5→51.46 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→51.46 Å
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Refine LS restraints |
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LS refinement shell |
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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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