+Open data
-Basic information
Entry | Database: PDB / ID: 6hoi | |||||||||
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Title | Structure of Beclin1 LIR motif bound to GABARAPL1 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Autophagy / ATG8 / LIR | |||||||||
Function / homology | Function and homology information cellular response to aluminum ion / glycophagy / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization ...cellular response to aluminum ion / glycophagy / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation of autophagosome assembly / engulfment of apoptotic cell / negative regulation of autophagosome assembly / receptor catabolic process / Tat protein binding / GABA receptor binding / protein targeting to lysosome / suppression by virus of host autophagy / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / : / SMAD protein signal transduction / phosphatidylinositol-3-phosphate biosynthetic process / Macroautophagy / autophagy of mitochondrion / mitotic metaphase chromosome alignment / lysosome organization / beta-tubulin binding / positive regulation of cardiac muscle hypertrophy / mitophagy / neuron development / p38MAPK cascade / autophagosome maturation / autophagosome membrane / autophagosome assembly / autophagosome / negative regulation of reactive oxygen species metabolic process / regulation of macroautophagy / response to vitamin E / cellular response to glucose starvation / cellular defense response / phosphatidylinositol 3-kinase binding / phagocytic vesicle / amyloid-beta metabolic process / positive regulation of autophagy / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / positive regulation of intrinsic apoptotic signaling pathway / regulation of cytokinesis / regulation of autophagy / phospholipid binding / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / trans-Golgi network / cytoplasmic vesicle membrane / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / protein-macromolecule adaptor activity / GTPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / defense response to virus / microtubule / response to hypoxia / nuclear body / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / Ub-specific processing proteases / endosome / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / dendrite / apoptotic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / endoplasmic reticulum / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | |||||||||
Authors | Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. ...Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. / Lamark, T. / Johansen, T. | |||||||||
Funding support | Norway, 2items
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Citation | Journal: Autophagy / Year: 2019 Title: Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs. Authors: Birgisdottir, A.B. / Mouilleron, S. / Bhujabal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S.A. / Lamark, T. / Johansen, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hoi.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hoi.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/6hoi ftp://data.pdbj.org/pub/pdb/validation_reports/ho/6hoi | HTTPS FTP |
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-Related structure data
Related structure data | 6hogC 6hohC 6hojC 6hokC 6holC 2r2qS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14598.667 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8 #2: Protein/peptide | Mass: 1038.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457 #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: 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: 1.94 Å3/Da / Density % sol: 36.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→35.161 Å / Num. obs: 88324 / % possible obs: 99.34 % / Redundancy: 4.1 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.01 / Rrim(I) all: 0.03 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.14→1.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8545 / CC1/2: 0.58 / Rpim(I) all: 0.44 / Rrim(I) all: 0.78 / % possible all: 97.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2R2Q Resolution: 1.14→35.161 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→35.161 Å
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Refine LS restraints |
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LS refinement shell |
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