+Open data
-Basic information
Entry | Database: PDB / ID: 3nih | ||||||
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Title | The structure of UBR box (RIAAA) | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / E3 ubiquitin ligase / UBR box / Zinc-binding protein / N-end rule / Ligase | ||||||
Function / homology | Function and homology information regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process ...regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / protein monoubiquitination / ubiquitin ligase complex / : / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Choi, W.S. / Jeong, B.-C. / Lee, M.-R. / Song, H.K. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases Authors: Choi, W.S. / Jeong, B.-C. / Joo, Y.J. / Lee, M.-R. / Kim, J. / Eck, M.J. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nih.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nih.ent.gz | 20 KB | Display | PDB format |
PDBx/mmJSON format | 3nih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/3nih ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3nih | HTTPS FTP |
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-Related structure data
Related structure data | 3niiC 3nijC 3nikC 3nilC 3nimC 3ninC 3nisSC 3nitC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9236.394 Da / Num. of mol.: 1 / Fragment: UBR-type domain, residues 115-194 Source method: isolated from a genetically manipulated source Details: UBR box Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P19812 | ||
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#2: Protein/peptide | Mass: 501.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % / Mosaicity: 0.696 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.16M ammonium acetate, 0.01M calcium chloride dihydrate, 0.05M sodium cacodylate trihydrate pH 6.5, 8%(w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 25, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 7049 / % possible obs: 99.8 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.077 / Χ2: 2.217 / Net I/σ(I): 12.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NIS Resolution: 2.1→37.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.56 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.192 / 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 max: 78.5 Å2 / Biso mean: 59.135 Å2 / Biso min: 33.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.1938 Å / Origin y: 9.7354 Å / Origin z: -6.8215 Å
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