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Yorodumi- PDB-1w4u: NMR solution structure of the ubiquitin conjugating enzyme UbcH5B -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w4u | ||||||
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Title | NMR solution structure of the ubiquitin conjugating enzyme UbcH5B | ||||||
Components | UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 | ||||||
Keywords | LIGASE / UBIQUITINATION / E2 ENZYME / BL CONJUGATION PATHWAY | ||||||
Function / homology | Function and homology information Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Inactivation of CSF3 (G-CSF) signaling / IKK complex recruitment mediated by RIP1 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Downstream TCR signaling / Peroxisomal protein import / (E3-independent) E2 ubiquitin-conjugating enzyme ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Inactivation of CSF3 (G-CSF) signaling / IKK complex recruitment mediated by RIP1 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Downstream TCR signaling / Peroxisomal protein import / (E3-independent) E2 ubiquitin-conjugating enzyme / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / 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 | SOLUTION NMR / ARIA | ||||||
Authors | Houben, K. / Dominguez, C. / Van Schaik, F.M.A. / Timmers, H.T.M. / Bonvin, A.M.J.J. / Boelens, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Solution Structure of the Ubiquitin-Conjugating Enzyme Ubch5B Authors: Houben, K. / Dominguez, C. / Van Schaik, F.M.A. / Timmers, H.T.M. / Bonvin, A.M.J.J. / Boelens, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w4u.cif.gz | 507.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w4u.ent.gz | 428.1 KB | Display | PDB format |
PDBx/mmJSON format | 1w4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w4u ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w4u | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16755.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P51669, UniProt: P62837*PLUS, ubiquitin-protein ligase |
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Compound details | CATALYZES THE COVALENT ATTACHMENT |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: NONE |
-Sample preparation
Details | Contents: 20MM KPI, 150MM KCL, 0.01MM ZNCL2, 10%D2O, UBCH5B 0.3MM |
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Sample conditions | Ionic strength: 150 mM / pH: 7.0 / Temperature: 300.0 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: ARIA / Software ordinal: 1 | |||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 10 |