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Open data
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Basic information
Entry | Database: PDB / ID: 5yip | ||||||
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Title | Crystal Structure of AnkG LIR/GABARAPL1 complex | ||||||
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![]() | SIGNALING PROTEIN / Autophagy | ||||||
Function / homology | ![]() positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / regulation of protein targeting / maintenance of protein location in plasma membrane / substrate localization to autophagosome / membrane assembly / Macroautophagy / protein localization to axon / clustering of voltage-gated sodium channels ...positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / regulation of protein targeting / maintenance of protein location in plasma membrane / substrate localization to autophagosome / membrane assembly / Macroautophagy / protein localization to axon / clustering of voltage-gated sodium channels / positive regulation of sodium ion transmembrane transporter activity / establishment or maintenance of microtubule cytoskeleton polarity / regulation of potassium ion transport / spectrin-associated cytoskeleton / magnesium ion homeostasis / glycophagy / positive regulation of membrane potential / negative regulation of delayed rectifier potassium channel activity / plasma membrane organization / phosphorylation-dependent protein binding / positive regulation of homotypic cell-cell adhesion / positive regulation of cation channel activity / autophagy of mitochondrion / maintenance of protein location in cell / Tat protein binding / axon initial segment / GABA receptor binding / paranode region of axon / positive regulation of sodium ion transport / Golgi to plasma membrane protein transport / negative regulation of endocytosis / node of Ranvier / costamere / cellular response to magnesium ion / regulation of modification of postsynaptic structure / anterograde axonal transport / cellular response to nitrogen starvation / spectrin binding / neuromuscular junction development / axon development / autophagosome membrane / mitotic cytokinesis / intercalated disc / neuronal action potential / response to immobilization stress / autophagosome assembly / autophagosome / lateral plasma membrane / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / axon cytoplasm / T-tubule / dendrite membrane / cytoskeletal protein binding / dendrite cytoplasm / axonogenesis / basal plasma membrane / sarcoplasmic reticulum / axon guidance / protein localization to plasma membrane / macroautophagy / synapse organization / establishment of protein localization / cytoplasmic vesicle membrane / neuromuscular junction / structural constituent of cytoskeleton / sarcolemma / Z disc / positive regulation of non-canonical NF-kappaB signal transduction / protein-macromolecule adaptor activity / cell body / basolateral plasma membrane / postsynaptic membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / postsynapse / microtubule / lysosome / cytoskeleton / neuron projection / cadherin binding / axon / glutamatergic synapse / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / Golgi apparatus / cell surface / signal transduction / endoplasmic reticulum / mitochondrion / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, J. / Zhu, R. / Chen, K. / Zheng, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins. Authors: Li, J. / Zhu, R. / Chen, K. / Zheng, H. / Zhao, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.3 KB | Display | ![]() |
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PDB format | ![]() | 56 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yiqC ![]() 5yirC ![]() 5yisC ![]() 2r2qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 14642.653 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2919.998 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1985-2010 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 4.6 Details: 35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 18077 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 27.51 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.022 / Rrim(I) all: 0.087 / Χ2: 0.529 / Net I/σ(I): 4.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2R2Q Resolution: 1.85→30.118 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.07 Å2 / Biso mean: 37.7709 Å2 / Biso min: 17.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→30.118 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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