+Open data
-Basic information
Entry | Database: PDB / ID: 3vh3 | ||||||
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Title | Crystal structure of Atg7CTD-Atg8 complex | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/PROTEIN TRANSPORT / autophagy / E1 / zinc binding / METAL BINDING PROTEIN-PROTEIN TRANSPORT complex | ||||||
Function / homology | Function and homology information Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / protein modification by small protein conjugation / C-terminal protein lipidation / vacuole-isolation membrane contact site ...Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / protein modification by small protein conjugation / C-terminal protein lipidation / 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 / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein-containing complex localization / phagophore assembly site / fungal-type vacuole membrane / reticulophagy / autophagosome membrane / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / mitochondrial membrane / macroautophagy / protein tag activity / autophagy / protein transport / membrane fusion / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Noda, N.N. / Satoo, K. / Inagaki, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: Structural basis of Atg8 activation by a homodimeric E1, Atg7. Authors: Noda, N.N. / Satoo, K. / Fujioka, Y. / Kumeta, H. / Ogura, K. / Nakatogawa, H. / 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 | 3vh3.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vh3.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/3vh3 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/3vh3 | HTTPS FTP |
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-Related structure data
Related structure data | 2li5C 3vh1SC 3vh2C 3vh4C 2zpnS S: Starting model for refinement C: citing same article (ref.) |
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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: 38150.859 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP RESIDUES 295-630) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: ATG7, APG7, CVT2, YHR171W / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P38862 |
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#2: Protein | Mass: 13751.865 Da / Num. of mol.: 1 / Mutation: K26P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P38182 |
#3: Chemical | ChemComp-ZN / |
#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: 2.59 Å3/Da / Density % sol: 52.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEGMME 5000, 5% tacsimate, 0.1M HEPES , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 38036 / Num. obs: 37933 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 53.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZPN, 3VH1 Resolution: 2→33.28 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 169287.11 / 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: 57.1183 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→33.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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