+Open data
-Basic information
Entry | Database: PDB / ID: 6kbm | ||||||
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Title | Crystal structure of Vac8 bound to Atg13 | ||||||
Components |
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Keywords | PROTEIN BINDING/PROTEIN TRANSPORT / Armadillo repeats / complex / PROTEIN BINDING-PROTEIN TRANSPORT complex | ||||||
Function / homology | Function and homology information nucleus-vacuole junction assembly / Cvt vesicle assembly / PAS complex / Myo2p-Vac17p-Vac8p transport complex / : / protein localization to membrane raft / regulation of cellular localization / nucleus-vacuole junction / ribophagy / vacuole-isolation membrane contact site ...nucleus-vacuole junction assembly / Cvt vesicle assembly / PAS complex / Myo2p-Vac17p-Vac8p transport complex / : / protein localization to membrane raft / regulation of cellular localization / nucleus-vacuole junction / ribophagy / vacuole-isolation membrane contact site / Atg1/ULK1 kinase complex / vacuole inheritance / vacuole fusion, non-autophagic / protein targeting to vacuole involved in autophagy / Macroautophagy / pexophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / protein kinase regulator activity / fungal-type vacuole membrane / phagophore assembly site / nuclear outer membrane / extrinsic component of membrane / response to starvation / activation of protein kinase activity / mitophagy / autophagosome assembly / positive regulation of autophagy / protein-membrane adaptor activity / macroautophagy / lipid metabolic process / autophagy / membrane raft / protein phosphorylation / lipid binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å | ||||||
Authors | Park, J. / Lee, C. | ||||||
Citation | Journal: Autophagy / Year: 2020 Title: Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways. Authors: Park, J. / Kim, H.I. / Jeong, H. / Lee, M. / Jang, S.H. / Yoon, S.Y. / Kim, H. / Park, Z.Y. / Jun, Y. / Lee, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kbm.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kbm.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/6kbm ftp://data.pdbj.org/pub/pdb/validation_reports/kb/6kbm | HTTPS FTP |
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-Related structure data
Related structure data | 6kbnC 5xjgS 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: 55339.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P39968 |
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#2: Protein | Mass: 14249.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: Q06628 |
#3: 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: 2.91 Å3/Da / Density % sol: 57.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, Tris, Ethylene glycol, PEG 3350, DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 17745 / % possible obs: 95.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.27 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.435 / Num. unique obs: 794 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XJG Resolution: 2.902→32.841 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.902→32.841 Å
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Refine LS restraints |
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LS refinement shell |
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