+Open data
-Basic information
Entry | Database: PDB / ID: 1umh | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis of sugar-recognizing ubiquitin ligase | ||||||
Components | F-box only protein 2 | ||||||
Keywords | LIGASE / UBIQUITIN / SCF / UBIQUITIN LIGASE / LECTIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information 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-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / regulation of protein ubiquitination / : ...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-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / regulation of protein ubiquitination / : / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / dendritic spine / protein ubiquitination / negative regulation of cell population proliferation / glutamatergic synapse / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Mizushima, T. / Hirao, T. / Yoshida, Y. / Lee, S.J. / Chiba, T. / Iwai, K. / Yamaguchi, Y. / Kato, K. / Tsukihara, T. / Tanaka, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: NAT.STRUCT.MOL.BIOL. / Year: 2004 Title: Structural basis of sugar-recognizing ubiquitin ligase Authors: Mizushima, T. / Hirao, T. / Yoshida, Y. / Lee, S.J. / Chiba, T. / Iwai, K. / Yamaguchi, Y. / Kato, K. / Tsukihara, T. / Tanaka, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1umh.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1umh.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 1umh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1umh ftp://data.pdbj.org/pub/pdb/validation_reports/um/1umh | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21021.010 Da / Num. of mol.: 1 / Fragment: SBD DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: mouse / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q80UW2, ubiquitin-protein ligase |
---|---|
#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.82 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris, PEG400, Nickel Chloride, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 20, 2002 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 18483 / Num. obs: 18483 / % possible obs: 99.9 % |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.1 % / Num. unique all: 2647 / Rsym value: 0.278 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2→54.23 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.72 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.192 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→54.23 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20 /
|