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Open data
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Basic information
Entry | Database: PDB / ID: 6kbn | ||||||
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Title | Crystal structure of Vac8 (del 19-33) bound to Atg13 | ||||||
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![]() | PROTEIN BINDING/PROTEIN TRANSPORT / Armadillo repeats / complex / PROTEIN BINDING-PROTEIN TRANSPORT complex | ||||||
Function / homology | ![]() nucleus-vacuole junction assembly / Cvt vesicle assembly / PAS complex / Myo2p-Vac17p-Vac8p transport complex / : / protein localization to membrane raft / nucleus-vacuole junction / regulation of cellular localization / vacuole-isolation membrane contact site / ribophagy ...nucleus-vacuole junction assembly / Cvt vesicle assembly / PAS complex / Myo2p-Vac17p-Vac8p transport complex / : / protein localization to membrane raft / nucleus-vacuole junction / regulation of cellular localization / vacuole-isolation membrane contact site / ribophagy / vacuole inheritance / protein targeting to vacuole involved in autophagy / Atg1/ULK1 kinase complex / vacuole fusion, non-autophagic / Macroautophagy / pexophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / protein kinase regulator activity / fungal-type vacuole membrane / nuclear outer membrane / phagophore assembly site / extrinsic component of membrane / activation of protein kinase activity / response to starvation / mitophagy / autophagosome assembly / positive regulation of autophagy / protein-membrane adaptor activity / macroautophagy / lipid metabolic process / autophagy / membrane raft / protein phosphorylation / lipid binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, J. / Lee, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 419.8 KB | Display | ![]() |
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PDB format | ![]() | 348.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.3 KB | Display | ![]() |
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Full document | ![]() | 493.8 KB | Display | |
Data in XML | ![]() | 39.5 KB | Display | |
Data in CIF | ![]() | 53.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kbmC ![]() 5xjgS 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: 61676.777 Da / Num. of mol.: 2 / Mutation: residues 19-33 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Protein | Mass: 14249.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG 3350, N-(2-Acetamido)iminodiacetic acid, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
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: 3.2→50 Å / Num. obs: 27903 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 17.88 |
Reflection shell | Resolution: 3.2→3.26 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 1320 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XJG Resolution: 3.2→35.113 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→35.113 Å
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Refine LS restraints |
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LS refinement shell |
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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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