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Yorodumi- PDB-3vxw: Crystal structure of Saccharomyces cerevisiae Atg8 complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vxw | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Atg8 complexed with Atg32 AIM | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ubiquitin fold / mitophagy | ||||||
Function / homology | Function and homology information Cvt vesicle membrane / TBC/RABGAPs / mitochondria-nucleus signaling pathway / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy ...Cvt vesicle membrane / TBC/RABGAPs / mitochondria-nucleus signaling pathway / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / protein-containing complex localization / phosphatidylethanolamine binding / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / vacuolar membrane / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / mitochondrial membrane / autophagy / protein tag activity / mitochondrial outer membrane / membrane fusion / ubiquitin protein ligase binding / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Noda, N.N. / Inagaki, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Autophagy-related protein 32 acts as autophagic degron and directly initiates mitophagy Authors: Kondo-Okamoto, N. / Noda, N.N. / Suzuki, S.W. / Nakatogawa, H. / Takahashi, I. / Matsunami, M. / Hashimoto, A. / Inagaki, F. / Ohsumi, Y. / Okamoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vxw.cif.gz | 36.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vxw.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vxw_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 3vxw_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 3vxw_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3vxw_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxw ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxw | HTTPS FTP |
-Related structure data
Related structure data | 2zpnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13757.894 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APG8, ATG8, AUT7, CVT5, YBL0732, YBL078C / Plasmid: pHT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P38182 | ||
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#2: Protein/peptide | Mass: 731.796 Da / Num. of mol.: 1 / Fragment: Atg8-family interacting motif / Source method: obtained synthetically Details: This sequence corresponds to residues 86-90 of Saccharomyces cerevisiae Atg32 Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40458 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 2.4M ammnonium sulfate, 0.1M sodium sulfate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 3969 / Num. obs: 3969 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.069 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 7.4 % / Num. unique all: 384 / Rsym value: 0.38 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZPN Resolution: 3→42.8 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 132387.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.4316 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→42.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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