+Open data
-Basic information
Entry | Database: PDB / ID: 6hol | |||||||||
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Title | Structure of ATG14 LIR motif bound to GABARAPL1 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Autophagy / ATG8 / LIR | |||||||||
Function / homology | Function and homology information extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / phosphatidylinositol 3-kinase complex, class III / glycophagy / mitochondria-associated endoplasmic reticulum membrane contact site / response to mitochondrial depolarisation / Tat protein binding / regulation of protein complex stability ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / phosphatidylinositol 3-kinase complex, class III / glycophagy / mitochondria-associated endoplasmic reticulum membrane contact site / response to mitochondrial depolarisation / Tat protein binding / regulation of protein complex stability / GABA receptor binding / phagophore assembly site membrane / protein targeting to lysosome / early endosome to late endosome transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phagophore assembly site / phosphatidylinositol-3-phosphate biosynthetic process / post-transcriptional regulation of gene expression / Macroautophagy / autophagosome membrane docking / endosome to lysosome transport / beta-tubulin binding / axoneme / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / regulation of macroautophagy / cellular response to glucose starvation / protein-membrane adaptor activity / cellular response to starvation / phagocytic vesicle / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein phosphorylation / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of protein phosphorylation / cytoplasmic vesicle membrane / phospholipid binding / GTPase binding / microtubule / positive regulation of protein phosphorylation / ubiquitin protein ligase binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / endoplasmic reticulum / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 6hol.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hol.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hol_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 6hol_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 6hol_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6hol_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/6hol ftp://data.pdbj.org/pub/pdb/validation_reports/ho/6hol | HTTPS FTP |
-Related structure data
Related structure data | 6hogC 6hohC 6hoiC 6hojC 6hokC 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: 1748.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6ZNE5 #3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 1.96 Å3/Da / Density % sol: 37.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: 1M LiCl, 0.1M HEPES pH7, 20% PEG 6000 |
-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 10, 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: 1.4→41.485 Å / Num. obs: 45978 / % possible obs: 93.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.06 / Rrim(I) all: 0.1 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4496 / CC1/2: 0.46 / Rpim(I) all: 0.55 / Rrim(I) all: 0.9 / % possible all: 90.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2R2Q Resolution: 1.4→41.485 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→41.485 Å
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Refine LS restraints |
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LS refinement shell |
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