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Yorodumi- PDB-4gga: Structural Analysis of Human Cdc20 Supports Multi-site Degron Rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gga | ||||||
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Title | Structural Analysis of Human Cdc20 Supports Multi-site Degron Recognition by APC/C | ||||||
Components | Cell division cycle protein 20 homolog | ||||||
Keywords | CELL CYCLE / mitosis / securin / ubiquitination / WD40 | ||||||
Function / homology | Function and homology information metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins ...metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / anaphase-promoting complex binding / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like ligase-substrate adaptor activity / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / RHO GTPases Activate Formins / 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 / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / cell differentiation / Ub-specific processing proteases / protein ubiquitination / cell division / centrosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.044 Å | ||||||
Authors | Luo, X. / Tian, W. / Tomchick, D.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural analysis of human Cdc20 supports multisite degron recognition by APC/C. Authors: Tian, W. / Li, B. / Warrington, R. / Tomchick, D.R. / Yu, H. / Luo, X. #1: Journal: Mol.Cell / Year: 2007 Title: Cdc20: a WD40 activator for a cell cycle degradation machine Authors: Yu, H. #2: Journal: J.Biol.Chem. / Year: 2007 Title: KEN-box-dependent degradation of Bub1 spindle checkpoint kinase by the anaphase-promoting complex/cyclosome Authors: Qi, W. / Yu, H. #3: Journal: Dev.Cell / Year: 2001 Title: Mad2-independent inhibition of APC-Cdc20 by the mitotic checkpoint protein BubR1 Authors: Tang, Z. / Bharadwaj, R. / Li, B. / Yu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gga.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gga.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/4gga ftp://data.pdbj.org/pub/pdb/validation_reports/gg/4gga | HTTPS FTP |
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-Related 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: 46350.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12834 |
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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: 2.13 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 100 mM Na citrate, 15 % (w/v) PEG 6000, and 4% MPD, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2010 / Details: monochromator |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.044→68.589 Å / Num. all: 25867 / Num. obs: 24684 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 18.7 Å2 / Limit h max: 19 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 54 / Limit l min: 0 / Rmerge(I) obs: 0.222 / Net I/σ(I): 10 |
Reflection scale | Group code: 1 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.599 / Num. unique all: 1044 / % possible all: 83.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.044→38.347 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.41 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.81 Å2 / Biso mean: 23.3523 Å2 / Biso min: 3.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.044→38.347 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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