+Open data
-Basic information
Entry | Database: PDB / ID: 4tu3 | ||||||
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Title | Crystal structure of yeast Sac1/Vps74 complex | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN TRANSPORT / Protein Complex / Phosphoric Monoester Hydrolases / Phosphatidylinositol Phosphates / Golgi Apparatus / HYDROLASE-PROTEIN TRANSPORT complex | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the ER membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3-phosphatase / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Golgi vesicle budding / host cell viral assembly compartment / Synthesis of PIPs at the Golgi membrane ...Synthesis of PIPs at the ER membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3-phosphatase / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Golgi vesicle budding / host cell viral assembly compartment / Synthesis of PIPs at the Golgi membrane / protein O-linked mannosylation / SPOTS complex / intracellular sphingolipid homeostasis / Golgi cisterna / protein retention in Golgi apparatus / cortical endoplasmic reticulum / Golgi to plasma membrane protein transport / phosphatidylinositol dephosphorylation / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation / phosphatidylinositol-4-phosphate binding / Golgi cisterna membrane / Golgi organization / Golgi medial cisterna / endoplasmic reticulum unfolded protein response / trans-Golgi network / mitochondrial outer membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / enzyme binding / endoplasmic reticulum / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.187 Å | ||||||
Authors | Cai, Y. / Horenkamp, F.A. / Reinisch, K.R. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2014 Title: Sac1-Vps74 structure reveals a mechanism to terminate phosphoinositide signaling in the Golgi apparatus. Authors: Cai, Y. / Deng, Y. / Horenkamp, F. / Reinisch, K.M. / Burd, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tu3.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tu3.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 4tu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/4tu3 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/4tu3 | HTTPS FTP |
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-Related 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: 71214.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SAC1, RSD1, YKL212W / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) References: UniProt: P32368, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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#2: Protein | Mass: 39334.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: VPS74, YDR372C, D9481.15 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q06385 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 200mM HEPES at pH 7.0, 35% (v/v) MPD, 0.3M NDSB-195 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.187→29.542 Å / Num. obs: 22586 / % possible obs: 100 % / Redundancy: 9.8 % / Net I/σ(I): 18.8 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZIH, 3LWT Resolution: 3.187→29.542 Å / Cross valid method: NONE / σ(F): 2.01 / Phase error: 41.04 / Stereochemistry target values: TWIN_LSQ_F
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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: 3.187→29.542 Å
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Refine LS restraints |
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LS refinement shell |
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