[English] 日本語
Yorodumi- PDB-5jge: Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jge | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / Receptor / Complex | ||||||
Function / homology | Function and homology information aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / vesicle organization / phagophore assembly site membrane / fungal-type vacuole / protein-containing complex localization / phagophore assembly site / metalloaminopeptidase activity / ERAD pathway ...aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / vesicle organization / phagophore assembly site membrane / fungal-type vacuole / protein-containing complex localization / phagophore assembly site / metalloaminopeptidase activity / ERAD pathway / autophagy / protein transport / protein-macromolecule adaptor activity / proteolysis / zinc ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Watanabe, Y. / Noda, N.N. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates Authors: Yamasaki, A. / Watanabe, Y. / Adachi, W. / Suzuki, K. / Matoba, K. / Kirisako, H. / Kumeta, H. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F. / Noda, N.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jge.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jge.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jge_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jge_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 5jge_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5jge_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jge ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jge | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-Components
#1: Protein/peptide | Mass: 3804.433 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ATG19, CVT19, YOL082W, O0980, YOL01 / Production host: Escherichia coli (E. coli) / References: UniProt: P35193 #2: Protein/peptide | Mass: 2781.269 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P14904*PLUS #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.35 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% (w/v) PEG 4000, 200 mM sodium acetate, 100 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.0000, 0.9792 | |||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2012 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.9→55.33 Å / Num. obs: 13677 / % possible obs: 97.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14 | |||||||||
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.458 / % possible all: 96.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.91→55.33 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.881 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.716 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→55.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|