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Open data
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Basic information
Entry | Database: PDB / ID: 4gsl | ||||||
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Title | Crystal structure of an Atg7-Atg3 crosslinked complex | ||||||
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![]() | PROTEIN TRANSPORT / Ubiquitin-like protein activation enzyme / Ubiquitin-like protein transfer enzyme | ||||||
Function / homology | ![]() Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / phagophore / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway ...Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / phagophore / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phagophore assembly site / protein targeting to membrane / Antigen processing: Ubiquitination & Proteasome degradation / autophagosome assembly / Neutrophil degranulation / macroautophagy / autophagy / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaiser, S.E. / Mao, K. / Taherbhoy, A.M. / Yu, S. / Olszewski, J.L. / Duda, D.M. / Kurinov, I. / Deng, A. / Fenn, T.D. / Klionsky, D.J. / Schulman, B.A. | ||||||
![]() | ![]() Title: Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Authors: Kaiser, S.E. / Mao, K. / Taherbhoy, A.M. / Yu, S. / Olszewski, J.L. / Duda, D.M. / Kurinov, I. / Deng, A. / Fenn, T.D. / Klionsky, D.J. / Schulman, B.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 638.9 KB | Display | ![]() |
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PDB format | ![]() | 527.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468 KB | Display | ![]() |
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Full document | ![]() | 510.9 KB | Display | |
Data in XML | ![]() | 56 KB | Display | |
Data in CIF | ![]() | 75.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gsjC ![]() 4gskC ![]() 2dytS ![]() 3t7eS ![]() 3t7fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69692.211 Da / Num. of mol.: 2 / Fragment: UNP residues 1-613 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: APG7, ATG7, CVT2, YHR171W / Plasmid: pGEX-4T1 / Production host: ![]() ![]() #2: Protein | Mass: 35974.973 Da / Num. of mol.: 2 / Mutation: C41A, C76A, C83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: APG3, ATG3, AUT1, N2040, YNR007C / Plasmid: pGEX-4T1 / Production host: ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.31 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 100 mM sodium citrate, pH 5.8, 13.5% PEG4000, 10% isopropanol, 5% dioxane, 88 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→40 Å / Num. all: 65155 / Num. obs: 64845 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.079 / Χ2: 3.615 / Net I/σ(I): 17.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3T7E, 3T7F, AND 2DYT Resolution: 2.703→37.073 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.82 / σ(F): 0 / σ(I): 0 / Phase error: 24.14 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.889 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 224.79 Å2 / Biso mean: 70.5395 Å2 / Biso min: 13.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.703→37.073 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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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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