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Open data
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Basic information
Entry | Database: PDB / ID: 5yiq | ||||||
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Title | Crystal structure of AnkG LIR/LC3B complex | ||||||
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![]() | PROTEIN BINDING / Autophagy | ||||||
Function / homology | ![]() Receptor Mediated Mitophagy / 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 / membrane assembly / TBC/RABGAPs / Macroautophagy / protein localization to axon ...Receptor Mediated Mitophagy / 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 / membrane assembly / TBC/RABGAPs / Macroautophagy / protein localization to axon / Pexophagy / clustering of voltage-gated sodium channels / PINK1-PRKN Mediated Mitophagy / 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 / positive regulation of membrane potential / phosphorylation-dependent protein binding / plasma membrane organization / negative regulation of delayed rectifier potassium channel activity / mucus secretion / positive regulation of homotypic cell-cell adhesion / positive regulation of cation channel activity / maintenance of protein location in cell / KEAP1-NFE2L2 pathway / axon initial segment / paranode region of axon / positive regulation of sodium ion transport / Golgi to plasma membrane protein transport / cellular response to nitrogen starvation / negative regulation of endocytosis / node of Ranvier / costamere / cellular response to magnesium ion / phosphatidylethanolamine binding / anterograde axonal transport / positive regulation of mucus secretion / microtubule associated complex / autolysosome / neuromuscular junction development / spectrin binding / axon development / axoneme / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / intercalated disc / response to immobilization stress / mitotic cytokinesis / lateral plasma membrane / positive regulation of protein targeting to membrane / autophagosome / neuronal action potential / endomembrane system / axon cytoplasm / T-tubule / cytoskeletal protein binding / cellular response to starvation / tubulin binding / axonogenesis / basal plasma membrane / sarcoplasmic reticulum / establishment of localization in cell / protein localization to plasma membrane / mitochondrial membrane / axon guidance / synapse organization / establishment of protein localization / neuromuscular junction / structural constituent of cytoskeleton / sarcolemma / autophagy / Z disc / positive regulation of non-canonical NF-kappaB signal transduction / protein-macromolecule adaptor activity / cytoplasmic vesicle / microtubule binding / basolateral plasma membrane / postsynaptic membrane / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / lysosome / cytoskeleton / cadherin binding / neuron projection / protein domain specific binding / axon / neuronal cell body / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / cell surface / signal transduction / membrane 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 | ![]() | 43.9 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yipC ![]() 5yirC ![]() 5yisC ![]() 1ugmS 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: 14637.859 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-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.5 Details: 10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 6417 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.064 / Rrim(I) all: 0.149 / Χ2: 1.959 / Net I/σ(I): 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UGM Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.767 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.288 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.88 Å2 / Biso mean: 53.855 Å2 / Biso min: 28.6 Å2
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Refinement step | Cycle: final / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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