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Yorodumi- PDB-2zpn: The crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zpn | ||||||
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Title | The crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412-415) complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ubiquitin fold / Autophagy / Cytoplasmic vesicle / Lipoprotein / Membrane / Transport / Ubl conjugation pathway / Vacuole | ||||||
Function / homology | Function and homology information Cvt vesicle membrane / Cvt complex / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / vesicle organization / cytoplasm to vacuole targeting by the Cvt pathway ...Cvt vesicle membrane / Cvt complex / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / vesicle organization / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein-containing complex localization / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / autophagosome membrane / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / : / mitochondrial membrane / macroautophagy / protein tag activity / autophagy / protein-macromolecule adaptor activity / protein transport / membrane fusion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Noda, N.N. / Inagaki, F. | ||||||
Citation | Journal: Genes Cells / Year: 2008 Title: Structural basis of target recognition by Atg8/LC3 during selective autophagy Authors: Noda, N.N. / Kumeta, H. / Nakatogawa, H. / Satoo, K. / Adachi, W. / Ishii, J. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zpn.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zpn.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zpn ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zpn | HTTPS FTP |
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-Related structure data
Related structure data | 1gnuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 13757.894 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Plasmid: pHT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P38182 #2: Protein/peptide | Mass: 575.610 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: This sequence corresponds to residues 412-415 of Saccharomyces cerevisiae Atg19. References: UniProt: P35193*PLUS #3: Chemical | ChemComp-SO4 / #4: 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: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 2.0M ammonium sulfate, 0.1M sodium citrate, pH4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.1 Å / Num. all: 14927 / Num. obs: 14927 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.12 / Num. unique all: 1494 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GNU Resolution: 2.7→41.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 84615.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.0308 Å2 / ksol: 0.371913 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→41.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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