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Yorodumi- PDB-8t33: Crystal structure of K46 acetylated GABARAP in complex with the L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t33 | ||||||
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Title | Crystal structure of K46 acetylated GABARAP in complex with the LIR of TP53INP2/DOR | ||||||
Components |
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Keywords | PROTEIN BINDING / Autophagy / GABARAP acetylation / DOR LIR / TP53INP2 LIR | ||||||
Function / homology | Function and homology information negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy ...negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / sperm midpiece / ubiquitin binding / protein localization / PML body / microtubule cytoskeleton organization / osteoblast differentiation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / positive regulation of DNA-templated transcription / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 | 8t33.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t33.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t33_validation.pdf.gz | 6 MB | Display | wwPDB validaton report |
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Full document | 8t33_full_validation.pdf.gz | 6 MB | Display | |
Data in XML | 8t33_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 8t33_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/8t33 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/8t33 | HTTPS FTP |
-Related structure data
Related structure data | 8t31C 8t32C 8t35C 8t36C 8t4tC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14127.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95166 | ||||||
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#2: Protein/peptide | Mass: 1615.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6 | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10 % w/v PEG 3000, 0.2 M Zinc acetate dihydrate, 0.1 M Sodium acetate PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.522 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.522 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→45.87 Å / Num. obs: 39016 / % possible obs: 99.84 % / Redundancy: 4.4 % / CC1/2: 0.999 / Net I/σ(I): 23.94 |
Reflection shell | Resolution: 1.599→1.657 Å / Num. unique obs: 3866 / CC1/2: 0.961 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→45.87 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.97 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.1 Å2 / Biso mean: 20.9786 Å2 / Biso min: 8.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.599→45.87 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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