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- PDB-2e33: Structural basis for selection of glycosylated substrate by SCFFb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2.0E+33 | |||||||||
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Title | Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase | |||||||||
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![]() | LIGASE/HYDROLASE / ubiquitin / SCF / Fbs1 / RNaseB / LIGASE-HYDROLASE COMPLEX | |||||||||
Function / homology | ![]() extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / pancreatic ribonuclease / ribonuclease A activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / pancreatic ribonuclease / ribonuclease A activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of protein ubiquitination / RNA nuclease activity / ERAD pathway / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / nucleic acid binding / dendritic spine / lyase activity / defense response to Gram-positive bacterium / protein ubiquitination / negative regulation of cell population proliferation / glutamatergic synapse / endoplasmic reticulum / extracellular region / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mizushima, T. / Yoshida, Y. / Kumanomidou, T. / Hasegawa, Y. / Yamane, T. / Tanaka, K. | |||||||||
![]() | ![]() Title: Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase Authors: Mizushima, T. / Yoshida, Y. / Kumanomidou, T. / Hasegawa, Y. / Suzuki, A. / Yamane, T. / Tanaka, 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 | ![]() | 76.7 KB | Display | ![]() |
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PDB format | ![]() | 55.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2e31C ![]() 2e32C ![]() 1umhS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 22593.631 Da / Num. of mol.: 1 / Fragment: Residues 105-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0% (v/v) PEG 400, 0.1M HEPES, 2.1M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→149.1 Å / Num. obs: 15839 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5.2 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UMH Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.824 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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