+Open data
-Basic information
Entry | Database: PDB / ID: 4rg6 | ||||||
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Title | Crystal structure of APC3-APC16 complex | ||||||
Components |
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Keywords | PROTEIN BINDING / Asymmetric complex / TPR fplding / Protein assembly | ||||||
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 / metaphase/anaphase transition of mitotic cell cycle / Phosphorylation of the APC/C / protein K11-linked ubiquitination ...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 / metaphase/anaphase transition of mitotic cell cycle / 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 / mitotic spindle / kinetochore / spindle / CDK-mediated phosphorylation and removal of Cdc6 / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / protein ubiquitination / cell cycle / cell division / centrosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Yamaguchi, M. / Yu, S. / Miller, D.J. / Schulman, B.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Structure of an APC3-APC16 Complex: Insights into Assembly of the Anaphase-Promoting Complex/Cyclosome. Authors: Yamaguchi, M. / Yu, S. / Qiao, R. / Weissmann, F. / Miller, D.J. / VanderLinden, R. / Brown, N.G. / Frye, J.J. / Peters, 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 | 4rg6.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rg6.ent.gz | 158.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/4rg6 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/4rg6 | 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: 63892.691 Da / Num. of mol.: 2 / Fragment: UNP residues 1-180, 447-824 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30260 #2: Protein/peptide | | Mass: 5076.753 Da / Num. of mol.: 1 / Fragment: UNP residues 74-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC16, C10orf104 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96DE5 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.74 Å3/Da / Density % sol: 74.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, pH 6.0, 0.2M magnesium chloride, 8% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0716 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0716 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 37171 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.1 |
Reflection shell | Resolution: 3.3→3.42 Å / Rsym value: 0.829 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 19.124 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.853 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.696 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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