+Open data
-Basic information
Entry | Database: PDB / ID: 6hok | |||||||||
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Title | Structure of Beclin1 LIR (S96E) motif bound to GABARAP | |||||||||
Components | Beclin-1,Gamma-aminobutyric acid receptor-associated protein | |||||||||
Keywords | SIGNALING PROTEIN / Autophagy / ATG8 / LIR | |||||||||
Function / homology | Function and homology information cellular response to aluminum ion / 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 / positive regulation of protein K48-linked ubiquitination / 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 / 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 / positive regulation of protein K48-linked ubiquitination / 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 / regulation of Rac protein signal transduction / negative regulation of autophagosome assembly / receptor catabolic process / GABA receptor binding / protein targeting to lysosome / suppression by virus of host autophagy / early endosome to late endosome transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / late endosome to vacuole transport / SMAD protein signal transduction / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / TBC/RABGAPs / microtubule associated complex / phosphatidylinositol-3-phosphate biosynthetic process / Macroautophagy / mitotic metaphase chromosome alignment / lysosome organization / beta-tubulin binding / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / axoneme / smooth endoplasmic reticulum / autophagosome maturation / autophagosome membrane / mitophagy / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / neuron development / autophagosome / protein targeting / negative regulation of reactive oxygen species metabolic process / response to vitamin E / regulation of macroautophagy / cellular response to glucose starvation / cellular defense response / phosphatidylinositol 3-kinase binding / phagocytic vesicle / amyloid-beta metabolic process / positive regulation of autophagy / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to epidermal growth factor stimulus / sperm midpiece / cellular response to copper ion / cellular response to amino acid starvation / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / response to lead ion / trans-Golgi network / ISG15 antiviral mechanism / microtubule cytoskeleton organization / cellular response to hydrogen peroxide / autophagy / actin cytoskeleton / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / GTPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / chemical synaptic transmission / cytoplasmic vesicle / microtubule binding / protein-containing complex assembly / defense response to virus / microtubule / lysosome / response to hypoxia / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / endosome membrane / Ub-specific processing proteases / endosome / response to xenobiotic stimulus / cell division / negative regulation of cell population proliferation / Golgi membrane / dendrite / synapse / apoptotic process / ubiquitin protein ligase binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 | 6hok.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hok.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/6hok ftp://data.pdbj.org/pub/pdb/validation_reports/ho/6hok | HTTPS FTP |
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-Related structure data
Related structure data | 6hogC 6hohC 6hoiC 6hojC 6holC 1gnuS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14901.962 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14457, UniProt: O95166 | ||
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#2: Chemical | #3: 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: 3.89 Å3/Da / Density % sol: 68.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 100 mM TRIS pH 8.5, 10 % Glycerol |
-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: Aug 21, 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: 1.61→49.72 Å / Num. obs: 30838 / % possible obs: 99.01 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.04 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.61→1.66 Å / Redundancy: 7 % / Rmerge(I) obs: 1.16 / Num. unique obs: 2999 / CC1/2: 0.61 / Rpim(I) all: 0.47 / Rrim(I) all: 1.26 / % possible all: 96.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GNU Resolution: 1.61→57.416 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→57.416 Å
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Refine LS restraints |
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LS refinement shell |
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