+Open data
-Basic information
Entry | Database: PDB / ID: 7qqy | |||||||||
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Title | yeast Gid10 bound to Art2 Pro/N-degron | |||||||||
Components |
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Keywords | LIGASE / GID / Art2 / ubiquitin / E3 ligase / metabolism | |||||||||
Function / homology | Function and homology information protein catabolic process in the vacuole / GID complex / protein targeting to vacuole / vacuole / response to osmotic stress / extrinsic component of membrane / response to starvation / negative regulation of gluconeogenesis / protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | |||||||||
Authors | Chrustowicz, J. / Sherpa, D. / Schulman, B.A. | |||||||||
Funding support | European Union, 2items
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Citation | Journal: Embo Rep. / Year: 2022 Title: A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters. Authors: Langlois, C.R. / Beier, V. / Karayel, O. / Chrustowicz, J. / Sherpa, D. / Mann, M. / Schulman, B.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qqy.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qqy.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqy ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqy | HTTPS FTP |
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-Related structure data
Related structure data | 7ns3S S: Starting model for refinement |
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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: 26188.107 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: YGR066C / Production host: Escherichia coli (E. coli) / References: UniProt: P53242 |
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#2: Protein/peptide | Mass: 1004.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 18.5% PEG3350, 0.1 M Bis-Tris propane pH 6.0 and 0.2 M potassium chloride |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→40.52 Å / Num. obs: 57128 / % possible obs: 99.2 % / Redundancy: 12.6 % / CC1/2: 1 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.26→1.33 Å / Num. unique obs: 8755 / CC1/2: 0.9 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NS3 Resolution: 1.26→37.74 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6053 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→37.74 Å
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Refine LS restraints |
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LS refinement shell |
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