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Yorodumi- PDB-8t4t: Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t4t | ||||||
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Title | Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR | ||||||
Components | Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A chimera | ||||||
Keywords | PROTEIN BINDING / LC3A / Autophagy / DOR LIR / TP53INP2 LIR | ||||||
Function / homology | Function and homology information negative regulation of protein localization / cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / tissue homeostasis / cellular response to nitrogen starvation / SMAD protein signal transduction / phosphatidylethanolamine binding / response to iron(II) ion / autolysosome / Macroautophagy ...negative regulation of protein localization / cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / tissue homeostasis / cellular response to nitrogen starvation / SMAD protein signal transduction / phosphatidylethanolamine binding / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / organelle membrane / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / JNK cascade / cellular response to copper ion / PINK1-PRKN Mediated Mitophagy / cellular response to amino acid starvation / cellular response to starvation / ubiquitin binding / macroautophagy / response to lead ion / protein localization / phospholipid binding / PML body / cellular response to hydrogen peroxide / osteoblast differentiation / late endosome / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / microtubule binding / microtubule / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.359 Å | ||||||
Authors | Ali, M.G.H. / Wahba, H.M. / Cyr, N. / Omichinski, J.G. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Autophagy / Year: 2024 Title: Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR. Authors: Ali, M.G. / Wahba, H.M. / Igelmann, S. / Cyr, N. / Ferbeyre, G. / Omichinski, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t4t.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t4t.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 8t4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t4t_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 8t4t_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 8t4t_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 8t4t_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/8t4t ftp://data.pdbj.org/pub/pdb/validation_reports/t4/8t4t | HTTPS FTP |
-Related structure data
Related structure data | 8t31C 8t32C 8t33C 8t35C 8t36C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15722.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH, MAP1LC3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6, UniProt: Q9H492 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12.5% PEG3350, 0.2M NH4-citrate, 5% isopropanol, 0.1M MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.359→39.883 Å / Num. obs: 9618 / % possible obs: 89.74 % / Redundancy: 3 % / CC1/2: 0.995 / Net I/σ(I): 7.91 |
Reflection shell | Resolution: 2.359→2.444 Å / Num. unique obs: 508 / CC1/2: 0.123 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.359→39.883 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.89 / 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: 2.359→39.883 Å
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Refine LS restraints |
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LS refinement shell |
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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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