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Yorodumi- PDB-8gt9: Selective targeting of the Beclin 2-Atg14L coiled coil complex by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gt9 | ||||||
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Title | Selective targeting of the Beclin 2-Atg14L coiled coil complex by stapled peptides promotes autophagy and endolysosomal trafficking of GPCRs | ||||||
Components | Beclin-2 | ||||||
Keywords | STRUCTURAL PROTEIN / PI3KC3 complex / Beclin 2 / Autophagy | ||||||
Function / homology | Function and homology information G protein-coupled receptor catabolic process / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / late endosome to vacuole transport / phagophore assembly site / cellular response to nitrogen starvation / endosome to lysosome transport / autophagosome assembly / mitophagy / phosphatidylinositol 3-kinase binding ...G protein-coupled receptor catabolic process / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / late endosome to vacuole transport / phagophore assembly site / cellular response to nitrogen starvation / endosome to lysosome transport / autophagosome assembly / mitophagy / phosphatidylinositol 3-kinase binding / autophagy / protein-macromolecule adaptor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Qiu, X. / Zhao, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Autophagy / Year: 2023 Title: The potent BECN2-ATG14 coiled-coil interaction is selectively critical for endolysosomal degradation of GPRASP1/GASP1-associated GPCRs. Authors: Qiu, X. / Li, N. / Yang, Q. / Wu, S. / Li, X. / Pan, X. / Yamamoto, S. / Zhang, X. / Zeng, J. / Liao, J. / He, C. / Wang, R. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gt9.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gt9.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gt9_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 8gt9_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 8gt9_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 8gt9_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/8gt9 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/8gt9 | HTTPS FTP |
-Related structure data
Related structure data | 8gu7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10970.921 Da / Num. of mol.: 4 / Mutation: R243L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BECN2, BECN1L1, BECN1P1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW95 #2: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M ammonium sulfate, 0.1 M MES, pH6.5, and 10% Dioxane. |
-Data collection
Diffraction | Mean temperature: 289 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.91836 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91836 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→70.39 Å / Num. obs: 34484 / % possible obs: 90.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.282 / Num. unique obs: 4709 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→70 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.104 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.36 Å2 / Biso mean: 21.302 Å2 / Biso min: 9.2 Å2
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Refinement step | Cycle: final / Resolution: 2→70 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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