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Yorodumi- PDB-1i7k: CRYSTAL STRUCTURE OF HUMAN MITOTIC-SPECIFIC UBIQUITIN-CONJUGATING... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i7k | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN MITOTIC-SPECIFIC UBIQUITIN-CONJUGATING ENZYME, UBCH10 | ||||||
Components | UBIQUITIN-CONJUGATING ENZYME E2 H10 | ||||||
Keywords | LIGASE / ubiquitin conjugating enzyme | ||||||
Function / homology | Function and homology information positive regulation of exit from mitosis / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C ...positive regulation of exit from mitosis / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / exit from mitosis / E2 ubiquitin-conjugating enzyme / ubiquitin-like protein ligase binding / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / CDK-mediated phosphorylation and removal of Cdc6 / protein polyubiquitination / Separation of Sister Chromatids / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein ubiquitination / cell division / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Basavappa, R. / Lin, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural and functional analysis of the human mitotic-specific ubiquitin-conjugating enzyme, UbcH10. Authors: Lin, Y. / Hwang, W.C. / Basavappa, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i7k.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i7k.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i7k_validation.pdf.gz | 374.2 KB | Display | wwPDB validaton report |
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Full document | 1i7k_full_validation.pdf.gz | 378.9 KB | Display | |
Data in XML | 1i7k_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1i7k_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i7k ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i7k | HTTPS FTP |
-Related structure data
Related structure data | 2e2cS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19657.197 Da / Num. of mol.: 2 / Mutation: C114S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBCH10 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: O00762, ubiquitin-protein ligase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.06 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1500, sodium chloride, sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusionDetails: drop consists of equal amounts of protein and precipitant solutions | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2000 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 24518 / Num. obs: 24518 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 2.532 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.167 / Num. unique all: 2218 / % possible all: 88.8 |
Reflection shell | *PLUS % possible obs: 88.8 % / Num. unique obs: 2218 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E2C Resolution: 1.95→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.808 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.226 / Rfactor Rwork: 0.176 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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