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Yorodumi- PDB-4wa6: Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angst... -
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-Basic information
Entry | Database: PDB / ID: 4wa6 | |||||||||
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Title | Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution | |||||||||
Components |
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Keywords | hydrolase/transcription / Multi-Protein Complex / Hydrolase-transcription complex | |||||||||
Function / homology | Function and homology information RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Ub-specific processing proteases / mRNA export from nucleus / nuclear pore / enzyme activator activity / RNA splicing / transcription elongation by RNA polymerase II / P-body / regulation of protein localization / protein transport / chromatin organization / protein-containing complex assembly / transcription coactivator activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | |||||||||
Authors | Wolberger, C. / Yan, M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Authors: Wolberger, C. / Yan, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wa6.cif.gz | 564.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wa6.ent.gz | 466.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wa6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wa6_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 4wa6_full_validation.pdf.gz | 512 KB | Display | |
Data in XML | 4wa6_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 4wa6_validation.cif.gz | 67 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/4wa6 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/4wa6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ADBF
#1: Protein | Mass: 54033.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: UBP8, YMR223W, YM9959.05 / Production host: Escherichia coli (E. coli) / References: UniProt: P50102, ubiquitinyl hydrolase 1 #2: Protein | Mass: 11094.497 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SUS1, YBR111W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WNK7 |
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-SAGA-associated factor ... , 2 types, 4 molecules CGEH
#3: Protein | Mass: 11297.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YJM789 / Gene: SGF11, SCY_5678 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZWK1 #4: Protein | Mass: 10825.258 Da / Num. of mol.: 2 / Mutation: N59D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SGF73, YGL066W / Production host: Escherichia coli (E. coli) / References: UniProt: P53165 |
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-Non-polymers , 2 types, 154 molecules
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.034 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2013 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.034 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→47.41 Å / Num. obs: 59279 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→47.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 18.851 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.261 / 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: 36.681 Å2
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Refinement step | Cycle: 1 / Resolution: 2.36→47.41 Å
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