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Open data
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Basic information
Entry | Database: PDB / ID: 2ob4 | ||||||
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Title | Human Ubiquitin-Conjugating Enzyme CDC34 | ||||||
![]() | Ubiquitin-conjugating enzyme E2-32 kDa complementing | ||||||
![]() | LIGASE / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | ![]() positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / response to growth factor / negative regulation of cAMP-mediated signaling / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / cellular response to interferon-beta / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / response to growth factor / negative regulation of cAMP-mediated signaling / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / cellular response to interferon-beta / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G1/S transition of mitotic cell cycle / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear speck / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Sicheri, F. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.1 KB | Display | ![]() |
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PDB format | ![]() | 32.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 436.5 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y6lC ![]() 1yh2C ![]() 1yrvC ![]() 1zdnC ![]() 1zuoC ![]() 2a4dC ![]() 2a7lC ![]() 2awfC ![]() 2f4wC ![]() 2qgxC ![]() 2z5dC ![]() 3bzhC ![]() 3cegC C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 20500.164 Da / Num. of mol.: 1 / Fragment: Catalytic Domain: Residues 7-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: The protein was dissolved at 42 mg/ml in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol and 2 mM DTT. Crystals were grown in hanging drops by mixing 2 microL protein solution with 2 microL ...Details: The protein was dissolved at 42 mg/ml in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol and 2 mM DTT. Crystals were grown in hanging drops by mixing 2 microL protein solution with 2 microL well solution (28% PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, 1 mM DTT and 7.5 mM glycyl-glycyl-glycine) at 21 deg C. For cryoprotection, the crystals were soaked in the well solution supplemented with 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2005 Details: cylindrically bent ULE glass mirror with Pt and Pd coatings |
Radiation | Monochromator: cryo-cooled Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 7162 / Num. obs: 7162 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.82 % / Rsym value: 0.076 / Net I/σ(I): 2.64 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 417 / Rsym value: 0.32 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.773 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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