+Open data
-Basic information
Entry | Database: PDB / ID: 7q4y | |||||||||
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Title | human Gid4 bound to a Gly/N-peptide | |||||||||
Components | Glucose-induced degradation protein 4 homolog | |||||||||
Keywords | LIGASE / GID / CTLH / ubiquitin / E3 ligase | |||||||||
Function / homology | Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Glucose-induced degradation protein 4 homolog Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | |||||||||
Authors | Sherpa, D. / Chrustowicz, J. / Prabu, J.R. / Schulman, B.A. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2022 Title: Multifaceted N-Degron Recognition and Ubiquitylation by GID/CTLH E3 Ligases. Authors: Chrustowicz, J. / Sherpa, D. / Teyra, J. / Loke, M.S. / Popowicz, G.M. / Basquin, J. / Sattler, M. / Prabu, J.R. / Sidhu, S.S. / 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 | 7q4y.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q4y.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 7q4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/7q4y ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q4y | HTTPS FTP |
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-Related structure data
Related structure data | 7q50C 7q51C 6cdcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23583.209 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IVV7 #2: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 18% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Bis-Tris pH 7 |
-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 PILATUS 2M-F / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.5 |
Reflection | Resolution: 3.08→73.16 Å / Num. obs: 15664 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC1/2: 0.994 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3.08→3.26 Å / Num. unique obs: 2435 / CC1/2: 0.236 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CDC Resolution: 3.08→62.37 Å / Cross valid method: THROUGHOUT / σ(F): 85.11 / Phase error: 27.48 / 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: 3.08→62.37 Å
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Refine LS restraints |
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LS refinement shell |
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