+Open data
-Basic information
Entry | Database: PDB / ID: 6jwp | ||||||
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Title | crystal structure of EGOC | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / EGOC / roadblock domain / Gtr1 / TORC1 | ||||||
Function / homology | Function and homology information MTOR signalling / protein localization to vacuolar membrane / Gtr1-Gtr2 GTPase complex / Ragulator complex / phosphate ion transport / microautophagy / protein localization to vacuole / Amino acids regulate mTORC1 / TORC1 signaling / vacuolar acidification ...MTOR signalling / protein localization to vacuolar membrane / Gtr1-Gtr2 GTPase complex / Ragulator complex / phosphate ion transport / microautophagy / protein localization to vacuole / Amino acids regulate mTORC1 / TORC1 signaling / vacuolar acidification / endocytic recycling / fungal-type vacuole membrane / lysosome organization / transcription by RNA polymerase I / transcription by RNA polymerase III / positive regulation of TOR signaling / subtelomeric heterochromatin formation / regulation of receptor recycling / positive regulation of TORC1 signaling / cellular response to starvation / negative regulation of autophagy / cholesterol homeostasis / cellular response to amino acid stimulus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / late endosome / late endosome membrane / positive regulation of MAPK cascade / chromosome, telomeric region / membrane raft / GTPase activity / chromatin / GTP binding / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å | ||||||
Authors | Zhang, T. / Ding, J. | ||||||
Citation | Journal: Sci Adv / Year: 2019 Title: Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases. Authors: Zhang, T. / Peli-Gulli, M.P. / Zhang, Z. / Tang, X. / Ye, J. / De Virgilio, C. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jwp.cif.gz | 681.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jwp.ent.gz | 557.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/6jwp ftp://data.pdbj.org/pub/pdb/validation_reports/jw/6jwp | HTTPS FTP |
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-Related structure data
Related structure data | 3r7wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-GTP-binding protein ... , 2 types, 4 molecules AFBG
#1: Protein | Mass: 36117.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GTR1 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00582 #2: Protein | Mass: 39092.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GTR2 / Plasmid: pACYCDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53290 |
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-Protein , 3 types, 6 molecules CHDIEJ
#3: Protein | Mass: 14471.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Plasmid: pACYCDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02205 #4: Protein | Mass: 8104.935 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: Gtr2 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3E830 #5: Protein | Mass: 18371.877 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: EGO3 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38247 |
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-Non-polymers , 2 types, 6 molecules
#6: Chemical | #7: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.24 Å / Num. obs: 36895 / % possible obs: 68.9 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.2→3.38 Å / Rmerge(I) obs: 1.679 / Num. unique obs: 1853 / CC1/2: 0.461 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R7W Resolution: 3.2→49.24 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.841 / SU B: 70.207 / SU ML: 0.498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.645 / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.98 Å2 / Biso mean: 70.248 Å2 / Biso min: 23.76 Å2
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Refinement step | Cycle: final / Resolution: 3.2→49.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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