+Open data
-Basic information
Entry | Database: PDB / ID: 5azf | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of LGG-1 complexed with a WEEL peptide | |||||||||
Components |
| |||||||||
Keywords | PROTEIN BINDING / Autophagy / Ubiquitin-like | |||||||||
Function / homology | Function and homology information dauer larval development / Macroautophagy / Cvt complex / cellular response to toxic substance / vesicle organization / positive regulation of autophagosome assembly / xenophagy / phagophore assembly site membrane / GABA receptor binding / programmed cell death ...dauer larval development / Macroautophagy / Cvt complex / cellular response to toxic substance / vesicle organization / positive regulation of autophagosome assembly / xenophagy / phagophore assembly site membrane / GABA receptor binding / programmed cell death / plasma membrane repair / cellular response to nitrogen starvation / protein-containing complex localization / phagophore assembly site / autophagy of mitochondrion / autophagosome membrane / necroptotic process / autophagosome assembly / autophagosome / : / lysosomal lumen / determination of adult lifespan / macroautophagy / autophagy / phagocytic vesicle membrane / protein transport / protein-macromolecule adaptor activity / response to heat / perikaryon / mitochondrial outer membrane / neuron projection / defense response to Gram-positive bacterium / neuronal cell body / dendrite / ubiquitin protein ligase binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Watanabe, Y. / Noda, N.N. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy. Authors: Wu, F. / Watanabe, Y. / Guo, X.Y. / Qi, X. / Wang, P. / Zhao, H.Y. / Wang, Z. / Fujioka, Y. / Zhang, H. / Ren, J.Q. / Fang, T.C. / Shen, Y.X. / Feng, W. / Hu, J.J. / Noda, N.N. / Zhang, H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5azf.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5azf.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 5azf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/5azf ftp://data.pdbj.org/pub/pdb/validation_reports/az/5azf | HTTPS FTP |
---|
-Related structure data
Related structure data | 5azgC 5azhC 5e6nC 5e6oC 1eo6S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14279.358 Da / Num. of mol.: 2 / Fragment: UNP residues 1-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lgg-1, C32D5.9 / Plasmid: pGEX-6P / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q09490 #2: Protein/peptide | Mass: 575.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35193 #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.5 M Sodium acetate, 50 mM HEPES, 25 mM Cadmium sulfate |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.4 Å / Num. obs: 51705 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EO6 Resolution: 1.6→29.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 98719.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.2602 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→29.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|