[English] 日本語
Yorodumi- PDB-8gu7: Selective targeting of the Beclin 2-Atg14L coiled coil complex by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gu7 | ||||||
---|---|---|---|---|---|---|---|
Title | Selective targeting of the Beclin 2-Atg14L coiled coil complex by stapled peptides promotes autophagy and endolysosomal trafficking of GPCRs | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN / PI3KC3 complex / Beclin 2 / Autophagy | ||||||
Function / homology | Function and homology information G protein-coupled receptor catabolic process / extrinsic component of omegasome membrane / : / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / mitochondria-associated endoplasmic reticulum membrane contact site ...G protein-coupled receptor catabolic process / extrinsic component of omegasome membrane / : / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / mitochondria-associated endoplasmic reticulum membrane contact site / response to mitochondrial depolarisation / protein targeting to lysosome / phagophore assembly site membrane / late endosome to vacuole transport / early endosome to late endosome transport / phagophore assembly site / cellular response to nitrogen starvation / phosphatidylinositol-3-phosphate biosynthetic process / autophagosome membrane docking / post-transcriptional regulation of gene expression / endosome to lysosome transport / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / mitophagy / regulation of macroautophagy / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / phagocytic vesicle / autophagosome / cellular response to starvation / negative regulation of protein phosphorylation / macroautophagy / regulation of protein phosphorylation / autophagy / GTPase binding / protein-macromolecule adaptor activity / positive regulation of protein phosphorylation / protein phosphorylation / endoplasmic reticulum membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Qiu, X. / Zhao, Y. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gu7.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gu7.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gu7_validation.pdf.gz | 312.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8gu7_full_validation.pdf.gz | 313 KB | Display | |
Data in XML | 8gu7_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 8gu7_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/8gu7 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/8gu7 | HTTPS FTP |
-Related structure data
Related structure data | 8gt9SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7021.218 Da / Num. of mol.: 2 / Mutation: C22L,C34S,G36L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atg14, Atg14L, D14Ertd436e, Kiaa0831 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CDJ3 #2: Protein | Mass: 10970.921 Da / Num. of mol.: 2 / 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 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic, pH 7.0 |
---|
-Data collection
Diffraction | Mean temperature: 289 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51.26 Å / Num. obs: 6736 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.995 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Num. unique obs: 951 / CC1/2: 0.972 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8GT9 Resolution: 2.6→41.11 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / SU B: 0.012 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||
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: 172.69 Å2 / Biso mean: 66.999 Å2 / Biso min: 33.89 Å2
| ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→41.11 Å
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|