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Yorodumi- PDB-6n5y: Crystal structure of the SNX5 PX domain in complex with the CI-MP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n5y | ||||||
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Title | Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1) | ||||||
Components | Sorting nexin-5,Cation-independent mannose-6-phosphate receptor | ||||||
Keywords | ENDOCYTOSIS / sorting nexin / SNX / endosome | ||||||
Function / homology | Function and homology information retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity ...retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / 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 / retromer complex / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / retrograde transport, endosome to Golgi / lysosomal transport / phagocytic cup / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / dynactin binding / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / regulation of macroautophagy / animal organ regeneration / response to retinoic acid / positive regulation of insulin receptor signaling pathway / transport vesicle / ruffle / receptor-mediated endocytosis / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / intracellular protein transport / trans-Golgi network / cytoplasmic side of plasma membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / cadherin binding / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Collins, B. / Paul, B. / Weeratunga, S. | ||||||
Citation | Journal: Nat.Cell Biol. / Year: 2019 Title: Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins. Authors: Simonetti, B. / Paul, B. / Chaudhari, K. / Weeratunga, S. / Steinberg, F. / Gorla, M. / Heesom, K.J. / Bashaw, G.J. / Collins, B.M. / Cullen, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n5y.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n5y.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 6n5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n5y ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n5y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21024.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5, IGF2R, MPRI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3, UniProt: P11717 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 75% of 0.2 M (NH4)SO4, 0.1 M MES pH 6.5, 30% (w/v) PEG5000 MME + 15% glycerol + 30% v/v (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97803 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97803 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→49.1 Å / Num. obs: 10740 / % possible obs: 99.8 % / Redundancy: 12.9 % / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.26→2.33 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→49.1 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→49.1 Å
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Refine LS restraints |
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LS refinement shell |
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