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Yorodumi- PDB-1jhj: Crystal structure of the APC10/Doc1 subunit of the human anaphase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jhj | ||||||
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Title | Crystal structure of the APC10/Doc1 subunit of the human anaphase-promoting complex | ||||||
Components | APC10 | ||||||
Keywords | CELL CYCLE / beta sandwich / jellyroll | ||||||
Function / homology | Function and homology information 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 / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase ...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 / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / 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 / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / cell cycle / cell division / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Wendt, K.S. / Vodermaier, H.C. / Jacob, U. / Gieffers, C. / Gmachl, M. / Peters, J.-M. / Huber, R. / Sondermann, P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of the APC10/DOC1 subunit of the human anaphase-promoting complex Authors: Wendt, K.S. / Vodermaier, H.C. / Jacob, U. / Gieffers, C. / Gmachl, M. / Peters, J.M. / Huber, R. / Sondermann, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jhj.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jhj.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/1jhj ftp://data.pdbj.org/pub/pdb/validation_reports/jh/1jhj | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19499.959 Da / Num. of mol.: 1 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pUBS250 / References: UniProt: Q9UM13 |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: ammonium sulfate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9791, 0.9797, 0.9500, 1.4800, 1.600 | ||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 18, 2000 | ||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / % possible obs: 99.82 % / Observed criterion σ(I): 35.86 / Rmerge(I) obs: 0.047 / Net I/σ(I): 35.86 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→50 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→19.93 Å / Isotropic thermal model: Isotropic / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→19.93 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 500 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.209 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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