+Open data
-Basic information
Entry | Database: PDB / ID: 5v3n | ||||||
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Title | Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex | ||||||
Components |
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Keywords | HYDROLASE / monopolin / cohibin / rDNA silencing / desumoylation | ||||||
Function / homology | Function and homology information negative regulation of septation initiation signaling / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / rDNA binding / phosphatase activator activity ...negative regulation of septation initiation signaling / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / rDNA binding / phosphatase activator activity / rDNA heterochromatin formation / nucleolus organization / cysteine-type peptidase activity / nuclear envelope / nucleolus / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae x Saccharomyces kudriavzevii (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | SIngh, N. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Genes Dev. / Year: 2017 Title: Recruitment of a SUMO isopeptidase to rDNA stabilizes silencing complexes by opposing SUMO targeted ubiquitin ligase activity. Authors: Liang, J. / Singh, N. / Carlson, C.R. / Albuquerque, C.P. / Corbett, K.D. / Zhou, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v3n.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v3n.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 5v3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v3n_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 5v3n_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 5v3n_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 5v3n_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/5v3n ftp://data.pdbj.org/pub/pdb/validation_reports/v3/5v3n | HTTPS FTP |
-Related structure data
Related structure data | 5v1aC 3n4sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 12991.447 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CSM1, SPO86, YCR086W, YCR86W / Production host: Escherichia coli (E. coli) / References: UniProt: P25651 |
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#2: Protein/peptide | Mass: 4269.733 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae x Saccharomyces kudriavzevii (yeast), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: VIN7, ATCC 204508 / S288c / Gene: VIN7_2425, TOF2, YKR010C, YK109 / Production host: Escherichia coli (E. coli) / References: UniProt: H0GHZ9, UniProt: Q02208 |
#3: 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: 2.09 Å3/Da / Density % sol: 41.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium Acetate, 0.1 M HEPES pH 7.5 and 25% PEG 3350 and 25% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→42 Å / Num. obs: 33373 / % possible obs: 96.4 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.042 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 2.281 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.418 / Rpim(I) all: 1.418 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N4S Resolution: 1.3→35.115 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 32.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→35.115 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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