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- PDB-3o2p: A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o2p | ||||||
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Title | A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) | ||||||
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![]() | Ligase / Cell Cycle | ||||||
Function / homology | ![]() Iron uptake and transport / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / ubiquitin-like protein binding / regulation of metabolic process / positive regulation of glucose transmembrane transport / protein neddylation / ubiquitin conjugating enzyme binding / mitotic intra-S DNA damage checkpoint signaling ...Iron uptake and transport / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / ubiquitin-like protein binding / regulation of metabolic process / positive regulation of glucose transmembrane transport / protein neddylation / ubiquitin conjugating enzyme binding / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA replication origin binding / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / ubiquitin ligase complex / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / chromosome, telomeric region / protein ubiquitination / cell division / ubiquitin protein ligase binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scott, D.C. / Monda, J.K. / Grace, C.R.R. / Duda, D.M. / Kriwacki, R.W. / Kurz, T. / Schulman, B.A. | ||||||
![]() | ![]() Title: A dual E3 mechanism for Rub1 ligation to Cdc53. Authors: Scott, D.C. / Monda, J.K. / Grace, C.R. / Duda, D.M. / Kriwacki, R.W. / Kurz, T. / Schulman, B.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.8 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3o2uC ![]() 3o6bC ![]() 3bq3S 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: 24353.648 Da / Num. of mol.: 1 / Fragment: DCUN1 domain, residues 70-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DCN1, YLR128W, L3111 / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 10169.643 Da / Num. of mol.: 1 / Fragment: residues 730-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CDC53, YDL132W, D2190 / Production host: ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 27% PEG 3000, 0.1M Tris, 0.2M Lithium Sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. all: 15991 / Num. obs: 15730 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BQ3 Resolution: 2.233→33.065 Å / SU ML: 0.27 / σ(F): 0.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.759 Å2 / ksol: 0.381 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.233→33.065 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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