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Yorodumi- PDB-4w4u: Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w4u | |||||||||
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Title | Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution | |||||||||
Components |
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Keywords | transcription/hydrolase / Multi-Protein Complex / Hydrolase-transcription complex / transcription-hydrolase complex | |||||||||
Function / homology | Function and homology information RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / DNA binding, bending / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / DNA binding, bending / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / nuclear pore / enzyme activator activity / transcription elongation by RNA polymerase II / P-body / protein transport / chromatin organization / protein-containing complex assembly / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator activity / chromatin remodeling / regulation of transcription by RNA polymerase II / structural molecule activity / 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: 2.8 Å | |||||||||
Authors | Wolberger, C. / Yan, M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity. Authors: Yan, M. / Wolberger, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w4u.cif.gz | 544 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w4u.ent.gz | 449.9 KB | Display | PDB format |
PDBx/mmJSON format | 4w4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w4u_validation.pdf.gz | 490.1 KB | Display | wwPDB validaton report |
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Full document | 4w4u_full_validation.pdf.gz | 501.9 KB | Display | |
Data in XML | 4w4u_validation.xml.gz | 45 KB | Display | |
Data in CIF | 4w4u_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/4w4u ftp://data.pdbj.org/pub/pdb/validation_reports/w4/4w4u | HTTPS FTP |
-Related structure data
Related structure data | 3mhsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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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: CEN.PK113-7D / Gene: CENPK1137D_262 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P0J5, 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: CEN.PK113-7D / Gene: SUS1, CENPK1137D_4659 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P8F5 |
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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: CEN.PK113-7D / Gene: SGF11, CENPK1137D_1654 / Production host: Escherichia coli (E. coli) / References: UniProt: N1NXA6 #4: Protein | Mass: 10732.178 Da / Num. of mol.: 2 / Mutation: Y57A 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, 66 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: 2.04 Å3/Da / Density % sol: 39.79 % |
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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: May 18, 2013 |
Radiation | Monochromator: Double crystal cryo-cooled Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.034 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.02 Å / Num. obs: 34989 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 23.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MHS Resolution: 2.8→47.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 32.348 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / 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: 51.258 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→47.02 Å
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Refine LS restraints |
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