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Yorodumi- PDB-1y8x: Structural basis for recruitment of Ubc12 by an E2-binding domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y8x | ||||||
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Title | Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1 | ||||||
Components |
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Keywords | LIGASE / Ubiquitin-conjugating enzyme E2 M | ||||||
Function / homology | Function and homology information E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / protein neddylation / TGF-beta receptor signaling activates SMADs / post-translational protein modification / NIK-->noncanonical NF-kB signaling ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / protein neddylation / TGF-beta receptor signaling activates SMADs / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of cell cycle / protein heterodimerization activity / protein-containing complex / proteolysis / nucleoplasm / ATP binding / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Huang, D.T. / Paydar, A. / Zhuang, M. / Waddell, M.B. / Holton, J.M. / Schulman, B.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. Authors: Huang, D.T. / Paydar, A. / Zhuang, M. / Waddell, M.B. / Holton, J.M. / Schulman, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y8x.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y8x.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y8x ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y8x | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18485.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2M, UBC12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61081, ubiquitin-protein ligase |
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#2: Protein | Mass: 10856.974 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE1C, UBA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TBC4 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.11 % |
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-Data collection
Diffraction |
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Diffraction source |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 12655 / Num. obs: 12655 / Redundancy: 11.4 % / Rsym value: 0.099 / Net I/σ(I): 38.3 |
-Processing
Refinement | Method to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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