+Open data
-Basic information
Entry | Database: PDB / ID: 6a9y | ||||||
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Title | The crystal structure of Mu homology domain of SGIP1 | ||||||
Components | SH3-containing GRB2-like protein 3-interacting protein 1 | ||||||
Keywords | ENDOCYTOSIS / SGIP1 / dimer / disulfide bond | ||||||
Function / homology | Function and homology information positive regulation of feeding behavior / AP-2 adaptor complex / clathrin-dependent endocytosis / clathrin-coated vesicle / response to dietary excess / energy homeostasis / clathrin-coated pit / phospholipid binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis ...positive regulation of feeding behavior / AP-2 adaptor complex / clathrin-dependent endocytosis / clathrin-coated vesicle / response to dietary excess / energy homeostasis / clathrin-coated pit / phospholipid binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / microtubule binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Feng, Y. / Liu, X. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: SGIP1 dimerizes via intermolecular disulfide bond in mu HD domain during cellular endocytosis. Authors: Zhang, Y. / Feng, Y. / Xin, Y. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a9y.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a9y.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/6a9y ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a9y | HTTPS FTP |
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-Related structure data
Related structure data | 5awuS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 31269.523 Da / Num. of mol.: 1 / Fragment: Mu homology domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SGIP1 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q9BQI5 |
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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: 3.01 Å3/Da / Density % sol: 59.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1M Tris, pH 8.0, 3.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 10898 / % possible obs: 99.73 % / Redundancy: 6.5 % / Rsym value: 0.09 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 2.7→2.97 Å / Num. unique obs: 565 / Rsym value: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AWU Resolution: 2.7→29.912 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.912 Å
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Refine LS restraints |
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LS refinement shell |
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