+Open data
-Basic information
Entry | Database: PDB / ID: 5v1a | ||||||
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Title | Structure of S. cerevisiae Ulp2:Csm1 complex | ||||||
Components |
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Keywords | HYDROLASE / monopolin / rDNA silencing / SUMO isopeptidase / cohibin | ||||||
Function / homology | Function and homology information monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / SUMO is proteolytically processed / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / deSUMOylase activity / plasmid maintenance / protein desumoylation ...monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / SUMO is proteolytically processed / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / deSUMOylase activity / plasmid maintenance / protein desumoylation / homologous chromosome segregation / transcription elongation factor activity / chromosome condensation / mitotic spindle assembly checkpoint signaling / Major pathway of rRNA processing in the nucleolus and cytosol / cysteine-type peptidase activity / nuclear envelope / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nucleolus / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 | 5v1a.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v1a.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 5v1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/5v1a ftp://data.pdbj.org/pub/pdb/validation_reports/v1/5v1a | HTTPS FTP |
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-Related structure data
Related structure data | 5v3nC 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
#1: Protein/peptide | Mass: 2892.225 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: ULP2, SMT4, YIL031W / Production host: Escherichia coli (E. coli) / References: UniProt: P40537, Ulp1 peptidase |
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#2: Protein | Mass: 14139.714 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 |
#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 Å3/Da / Density % sol: 38.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→44 Å / Num. obs: 8129 / % possible obs: 98.7 % / Redundancy: 13.8 % / Rsym value: 0.053 / Net I/σ(I): 53.9 |
Reflection shell | Resolution: 2.14→2.2 Å / CC1/2: 0.699 / Rpim(I) all: 0.367 / Rsym value: 1.318 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N4S Resolution: 2.14→43.761 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→43.761 Å
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Refine LS restraints |
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LS refinement shell |
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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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