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Open data
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Basic information
Entry | Database: PDB / ID: 6hyo | ||||||
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Title | Structure of ULK1 LIR motif bound to GABARAP | ||||||
![]() | Serine/threonine-protein kinase ULK1,Gamma-aminobutyric acid receptor-associated protein | ||||||
![]() | SIGNALING PROTEIN / Autophagy / ATG8 / LIR | ||||||
Function / homology | ![]() omegasome membrane / neuron projection regeneration / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / positive regulation of autophagosome assembly / GABA receptor binding / phagophore assembly site membrane ...omegasome membrane / neuron projection regeneration / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / positive regulation of autophagosome assembly / GABA receptor binding / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / RAB GEFs exchange GTP for GDP on RABs / phosphatidylethanolamine binding / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / TBC/RABGAPs / reticulophagy / microtubule associated complex / Macroautophagy / Receptor Mediated Mitophagy / beta-tubulin binding / response to starvation / axoneme / cellular response to nutrient levels / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / sperm midpiece / macroautophagy / Regulation of TNFR1 signaling / peptidyl-threonine phosphorylation / protein localization / recycling endosome / small GTPase binding / autophagy / microtubule cytoskeleton organization / neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / GTPase binding / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / peptidyl-serine phosphorylation / microtubule / mitochondrial outer membrane / protein autophosphorylation / lysosome / non-specific serine/threonine protein kinase / negative regulation of cell population proliferation / axon / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / signal transduction / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mouilleron, S. / Wirth, M. / Zhang, W. / O'Reilly, N. / Tooze, S. / Johansen, T. / Razi, M. / Nyoni, L. / Joshi, D. | ||||||
![]() | ![]() Title: Molecular determinants regulating selective binding of autophagy adapters and receptors to ATG8 proteins. Authors: Wirth, M. / Zhang, W. / Razi, M. / Nyoni, L. / Joshi, D. / O'Reilly, N. / Johansen, T. / Tooze, S.A. / Mouilleron, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.5 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.9 KB | Display | ![]() |
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Full document | ![]() | 461.3 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hylC ![]() 6hymC ![]() 6hynC ![]() 1gnuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15935.272 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75385, UniProt: O95166, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M MgCl2. 0.1 M Na cacodylate pH 6.5, 20% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→41.12 Å / Num. obs: 74520 / % possible obs: 99.9 % / Redundancy: 18.6 % / Biso Wilson estimate: 14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.05 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.07→1.1 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.65 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7428 / CC1/2: 0.62 / Rpim(I) all: 0.44 / Rrim(I) all: 1.71 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GNU Resolution: 1.07→41.119 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→41.119 Å
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Refine LS restraints |
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LS refinement shell |
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