+Open data
-Basic information
Entry | Database: PDB / ID: 6hog | |||||||||
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Title | Structure of VPS34 LIR motif bound to GABARAP | |||||||||
Components | Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein | |||||||||
Keywords | SIGNALING PROTEIN / Autophagy / ATG8 / LIR | |||||||||
Function / homology | Function and homology information Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane ...Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / regulation of Rac protein signal transduction / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / GABA receptor binding / protein targeting to lysosome / early endosome to late endosome transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phosphatidylinositol-mediated signaling / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / microtubule associated complex / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / beta-tubulin binding / axoneme / smooth endoplasmic reticulum / autophagosome maturation / autophagosome membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / RHO GTPases Activate NADPH Oxidases / PI3K Cascade / autophagosome / protein targeting / regulation of macroautophagy / cellular response to glucose starvation / sperm midpiece / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / microtubule cytoskeleton organization / autophagy / endocytosis / peroxisome / phagocytic vesicle membrane / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / kinase activity / midbody / chemical synaptic transmission / cytoplasmic vesicle / microtubule binding / microtubule / lysosome / endosome / protein kinase activity / cell cycle / cell division / phosphorylation / Golgi membrane / synapse / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 | 6hog.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hog.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/6hog ftp://data.pdbj.org/pub/pdb/validation_reports/ho/6hog | HTTPS FTP |
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-Related structure data
Related structure data | 6hohC 6hoiC 6hojC 6hokC 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: 15191.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) References: UniProt: Q8NEB9, UniProt: O95166, phosphatidylinositol 3-kinase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.22 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES pH 7.1, 40% PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 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: 1.26→28.6 Å / Num. obs: 34959 / % possible obs: 99.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.01 / Rrim(I) all: 0.03 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.26→1.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10172 / CC1/2: 0.53 / Rpim(I) all: 0.49 / Rrim(I) all: 0.89 / % possible all: 98.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GNU Resolution: 1.26→28.6 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→28.6 Å
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Refine LS restraints |
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LS refinement shell |
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