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- PDB-2e31: 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+31 | ||||||
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Title | Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase | ||||||
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![]() | LIGASE / ubiquitin / SCF / ubiquitin ligase / fbs1 | ||||||
Function / homology | ![]() extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / F-box domain binding / PcG protein complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity ...extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / F-box domain binding / PcG protein complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / regulation of protein ubiquitination / ubiquitin-like ligase-substrate adaptor activity / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / ERAD pathway / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / beta-catenin binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / ubiquitin protein ligase activity / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / mitotic cell cycle / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / protein ubiquitination / chromatin remodeling / protein domain specific binding / negative regulation of cell population proliferation / centrosome / glutamatergic synapse / endoplasmic reticulum / nucleoplasm / nucleus / cytoplasm / cytosol 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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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ... BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). This molecule is a part of the SCF complex, which is a hetero tetramer generated by Skp1-Fbs1-Cul1-Rbx1. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
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PDB format | ![]() | 67.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e32C ![]() 2e33C ![]() 1ldkS ![]() 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: 33676.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 18972.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, 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: Oct 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→109.8 Å / Num. obs: 27964 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 52.83 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.7 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: SIR-AS, ![]() Starting model: PDB ENTRY 1LDK and 1UMH Resolution: 2.4→53.22 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.204 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.244 / 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: 66.935 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→53.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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