+Open data
-Basic information
Entry | Database: PDB / ID: 7bol | ||||||
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Title | ubiquitin-conjugating enzyme, Ube2D2 | ||||||
Components | Ubiquitin-conjugating enzyme E2 D2 | ||||||
Keywords | STRUCTURAL PROTEIN / ubiquitin-conjugating enzyme / Ube2D2 | ||||||
Function / homology | Function and homology information (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å | ||||||
Authors | Lee, S.O. / Ryu, K.S. / Chi, S.-W. | ||||||
Citation | Journal: Febs J. / Year: 2022 Title: MUL1-RING recruits the substrate, p53-TAD as a complex with UBE2D2-UB conjugate. Authors: Lee, M.S. / Lee, S.O. / Choi, J. / Ryu, M. / Lee, M.K. / Kim, J.H. / Hwang, E. / Lee, C.K. / Chi, S.W. / Ryu, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bol.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bol.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7bol ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7bol | HTTPS FTP |
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-Related structure data
Related structure data | 6m2cC 6m2dC 2eskS S: Starting model for refinement C: citing same article (ref.) |
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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: 16842.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
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#2: 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: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.5 M Ammonium sulfate 0.1 M Sodium citrate pH 5.6 1.0 M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2016 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.797→50 Å / Num. obs: 14967 / % possible obs: 96.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 15.47 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ESK Resolution: 1.797→26.476 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 20.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.25 Å2 / Biso mean: 18.3873 Å2 / Biso min: 5.22 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.797→26.476 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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