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Yorodumi- PDB-5awu: Crystal structure of the SGIP1 mu homology domain in complex with... -
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-Basic information
Entry | Database: PDB / ID: 5awu | |||||||||
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Title | Crystal structure of the SGIP1 mu homology domain in complex with an Eps15 fragment containing two DPF motifs (YDPFKGSDPFA) | |||||||||
Components |
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Keywords | ENDOCYTOSIS / Protein-protein interaction | |||||||||
Function / homology | Function and homology information positive regulation of feeding behavior / Golgi to endosome transport / AP-2 adaptor complex / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / aggresome ...positive regulation of feeding behavior / Golgi to endosome transport / AP-2 adaptor complex / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / aggresome / clathrin-coated vesicle / endosomal transport / positive regulation of receptor recycling / response to dietary excess / polyubiquitin modification-dependent protein binding / clathrin-coated pit / energy homeostasis / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / EGFR downregulation / Negative regulation of MET activity / phospholipid binding / positive regulation of receptor-mediated endocytosis / SH3 domain binding / endocytosis / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of cell population proliferation / early endosome membrane / microtubule binding / postsynapse / receptor-mediated endocytosis of virus by host cell / cadherin binding / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Shimada, A. / Yamaguchi, A. / Kohda, D. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 mu homology domain. Authors: Shimada, A. / Yamaguchi, A. / Kohda, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5awu.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5awu.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 5awu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/5awu ftp://data.pdbj.org/pub/pdb/validation_reports/aw/5awu | HTTPS FTP |
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-Related structure data
Related structure data | 5awrSC 5awsC 5awtC 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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Unit cell |
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-Components
#1: Protein | Mass: 30844.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 552-828 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SGIP1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQI5 | ||
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#2: Protein/peptide | Mass: 1244.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42566*PLUS | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 3350, zinc acetate, sodium acetate, sodium iodide PH range: 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 14137 / % possible obs: 99.8 % / Redundancy: 12 % / Net I/σ(I): 9.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AWR Resolution: 2.7→37.613 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→37.613 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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