+Open data
-Basic information
Entry | Database: PDB / ID: 5dfz | ||||||||||||
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Title | Structure of Vps34 complex II from S. cerevisiae. | ||||||||||||
Components |
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Keywords | TRANSFERASE / Vps34 / Vps15 / Vps30 / Vps38 / Autophagy / vacuolar protein sorting / Yeast / Complex II / PI3P / kinase / lipid / WD40 / BARA / C2 / coiled-coil / HEAT / nanobody | ||||||||||||
Function / homology | Function and homology information Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / lytic vacuole / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / Synthesis of PIPs at the Golgi membrane / vacuole-isolation membrane contact site / phosphatidylinositol 3-kinase complex, class III, type II / cellular response to potassium ion starvation / phosphatidylinositol 3-kinase complex, class III, type I ...Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / lytic vacuole / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / Synthesis of PIPs at the Golgi membrane / vacuole-isolation membrane contact site / phosphatidylinositol 3-kinase complex, class III, type II / cellular response to potassium ion starvation / phosphatidylinositol 3-kinase complex, class III, type I / vacuole inheritance / Macroautophagy / protein retention in Golgi apparatus / autophagy of peroxisome / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / protein targeting to vacuole / phagophore assembly site membrane / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / phosphatidylinositol biosynthetic process / retrograde transport, endosome to Golgi / phagophore assembly site / cellular response to nitrogen starvation / fungal-type vacuole membrane / phosphatidylinositol 3-kinase / SNARE complex assembly / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autophagosome assembly / mitophagy / phosphatidylinositol 3-kinase binding / SNARE binding / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / macroautophagy / autophagy / endocytosis / protein transport / late endosome / peroxisome / protein-macromolecule adaptor activity / non-specific serine/threonine protein kinase / endosome membrane / protein kinase activity / endosome / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / mitochondrion / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Lama glama (llama) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.4 Å | ||||||||||||
Authors | Rostislavleva, K. / Soler, N. / Ohashi, Y. / Zhang, L. / Williams, R.L. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Science / Year: 2015 Title: Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Authors: Rostislavleva, K. / Soler, N. / Ohashi, Y. / Zhang, L. / Pardon, E. / Burke, J.E. / Masson, G.R. / Johnson, C. / Steyaert, J. / Ktistakis, N.T. / Williams, R.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dfz.cif.gz | 464.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dfz.ent.gz | 312.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dfz_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 5dfz_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 5dfz_validation.xml.gz | 77.4 KB | Display | |
Data in CIF | 5dfz_validation.cif.gz | 108 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/5dfz ftp://data.pdbj.org/pub/pdb/validation_reports/df/5dfz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules AD
#1: Protein | Mass: 51072.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VPS38, VPL17, YLR360W, L8039.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05919 |
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#5: Protein | Mass: 63400.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VPS30, APG6, ATG6, VPT30, YPL120W, LPH7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02948 |
-Protein , 2 types, 2 molecules CB
#2: Protein | Mass: 100973.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VPS34, END12, PEP15, VPL7, VPT29, YLR240W, L9672.10 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22543, phosphatidylinositol 3-kinase |
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#3: Protein | Mass: 167082.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VPS15, GRD8, VAC4, VPL19, YBR097W, YBR0825 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P22219, non-specific serine/threonine protein kinase |
-Antibody / Protein/peptide , 2 types, 2 molecules EG
#4: Antibody | Mass: 13772.296 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#6: Protein/peptide | Mass: 4188.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 300 mM sodium acetate pH 5.1, 3% 1,5- Diaminopentanedihydrochloride. grown at 290 K for 5 days PH range: 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.939270, 1.254380, 1.254860 | ||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 4.4→49.9 Å / Num. all: 40224 / Num. obs: 40224 / % possible obs: 99.8 % / Redundancy: 32.2 % / Rsym value: 0.31 / Net I/σ(I): 21 | ||||||||||||
Reflection shell | Resolution: 4.4→4.58 Å / Redundancy: 15.8 % / Rmerge(I) obs: 4.82 / Mean I/σ(I) obs: 1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 4.4→50.358 Å / SU ML: 1.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 51.95 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.4→50.358 Å
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Refine LS restraints |
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LS refinement shell |
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