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- PDB-8grf: Crystal structure of F-box protein in the ternary complex with ad... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8grf | |||||||||
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Title | Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate | |||||||||
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![]() | TRANSFERASE/LIGASE / F-box protein / glyoxylate cycle / E3 ubiquitin ligase / TRANSFERASE / TRANSFERASE-LIGASE complex | |||||||||
Function / homology | ![]() citrate (Si)-synthase activity / citrate metabolic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / tricarboxylic acid cycle / mitotic cell cycle / carbohydrate metabolic process / protein ubiquitination / mitochondrial matrix / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nishio, K. / Nakatsukasa, K. / Kamura, T. / Mizushima, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Authors: Nishio, K. / Kawarasaki, T. / Sugiura, Y. / Matsumoto, S. / Konoshima, A. / Takano, Y. / Hayashi, M. / Okumura, F. / Kamura, T. / Mizushima, T. / Nakatsukasa, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 351.8 KB | Display | ![]() |
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PDB format | ![]() | 228.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.2 KB | Display | ![]() |
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Full document | ![]() | 488.1 KB | Display | |
Data in XML | ![]() | 46.8 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gqzC ![]() 8gr8C ![]() 8gr9C ![]() 8greC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51476.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CIT2, GI527_G0000583 / Production host: ![]() ![]() #2: Protein | | Mass: 42828.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: W303-1a / Production host: ![]() ![]() #3: Protein | | Mass: 22357.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SKP1, GI527_G0001262 / Production host: ![]() ![]() #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % Description: The entry contains friedel pairs in I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 70 mM Na citrate pH 5.5, 10.5% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→36.64 Å / Num. obs: 63124 / % possible obs: 99.24 % / Redundancy: 6.9 % / Biso Wilson estimate: 51.24 Å2 / CC1/2: 0.997 / Net I/σ(I): 24.58 |
Reflection shell | Resolution: 2.53→2.62 Å / Mean I/σ(I) obs: 4.09 / Num. unique obs: 6158 / CC1/2: 0.828 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The entry contains friedel pairs in I_plus/minus columns
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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: 60.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→36.64 Å
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Refine LS restraints |
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LS refinement shell |
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