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Yorodumi- PDB-2gjd: Distinct functional domains of Ubc9 dictate cell survival and res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gjd | ||||||
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Title | Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress | ||||||
Components | Ubiquitin-conjugating enzyme E2-18 kDa | ||||||
Keywords | LIGASE / Ubc9p / E2 / Smt3 / Saccharomyces Cerevisiae | ||||||
Function / homology | Function and homology information SUMO conjugating enzyme activity / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins ...SUMO conjugating enzyme activity / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of chromatin organization proteins / SUMO transferase activity / protein sumoylation / condensed nuclear chromosome / cell division / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | van Waardenburg, R.C. / Duda, D.M. / Lancaster, C.S. / Schulman, B.A. / Bjornsti, M.A. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2006 Title: Distinct functional domains of ubc9 dictate cell survival and resistance to genotoxic stress. Authors: van Waardenburg, R.C. / Duda, D.M. / Lancaster, C.S. / Schulman, B.A. / Bjornsti, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gjd.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gjd.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/2gjd ftp://data.pdbj.org/pub/pdb/validation_reports/gj/2gjd | HTTPS FTP |
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-Related structure data
Related structure data | 1u9aS 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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Details | The biological assembly consists of a crystallographic tetramer made up of molecules A,B,C, and D. |
-Components
#1: Protein | Mass: 17936.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC9 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P50623, ubiquitin-protein ligase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 6000, 0.1M HEPES, 0.1M NaBr, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. all: 65526 / Num. obs: 65226 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U9A Resolution: 1.75→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Xplor file |
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