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- PDB-3o6b: 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: 3o6b | ||||||
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Title | A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution | ||||||
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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 | ![]() | 263.6 KB | Display | ![]() |
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PDB format | ![]() | 217 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.3 KB | Display | ![]() |
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Full document | ![]() | 562.2 KB | Display | |
Data in XML | ![]() | 52.1 KB | Display | |
Data in CIF | ![]() | 70.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24353.648 Da / Num. of mol.: 5 / Fragment: DCUN1 domain, residues 70-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DCN1, YLR128W, L3111 / Production host: ![]() ![]() #2: Protein | Mass: 8652.943 Da / Num. of mol.: 5 / Fragment: residues 742-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CDC53, YDL132W, D2190 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 21% PEG 3350, 0.1M Bis-Tris-Propane, 0.2M NaF, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.1→40 Å / Num. all: 30487 / Num. obs: 30204 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.1→40 Å
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