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- PDB-4fip: Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fip | ||||||
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Title | Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module | ||||||
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![]() | HYDROLASE / Domain-swapping / Deubiquitination / Transcription / Nucleosomes | ||||||
Function / homology | ![]() 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 / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / transcription coactivator 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Samara, N.L. / Ringel, A.E. / Wolberger, C. | ||||||
![]() | ![]() Title: A Role for Intersubunit Interactions in Maintaining SAGA Deubiquitinating Module Structure and Activity. Authors: Samara, N.L. / Ringel, A.E. / Wolberger, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 537.2 KB | Display | ![]() |
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PDB format | ![]() | 442.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.8 KB | Display | ![]() |
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Full document | ![]() | 530 KB | Display | |
Data in XML | ![]() | 48.5 KB | Display | |
Data in CIF | ![]() | 66.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fjcC ![]() 4fk5C ![]() 3mhsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Biological assembly is a domain swapped dimer of a tetrameric complex. |
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Components
-Protein , 2 types, 4 molecules AEBF
#1: Protein | Mass: 54060.656 Da / Num. of mol.: 2 / Mutation: S144N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: UBP8, YM9959.05, YMR223W / Plasmid: pET-32a / Production host: ![]() ![]() #2: Protein | Mass: 11094.497 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SUS1, YBR111W-A / Plasmid: pRSF / Production host: ![]() ![]() |
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-SAGA-associated factor ... , 2 types, 4 molecules CGDH
#3: Protein | Mass: 8295.177 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-72 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SGF11, YPL047W / Plasmid: pCDFDuet / Production host: ![]() ![]() #4: Protein | Mass: 10824.273 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-96 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SGF73, YGL066W / Plasmid: pCDFDuet / Production host: ![]() ![]() |
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-Non-polymers , 2 types, 106 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2010 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.686→50 Å / Num. all: 47615 / Num. obs: 43495 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 12.227 |
Reflection shell | Resolution: 2.686→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.345 / Rsym value: 0.637 / % possible all: 84.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3MHS Resolution: 2.686→47.18 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 26.775 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / 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: 44.481 Å2
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Refinement step | Cycle: LAST / Resolution: 2.686→47.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.686→2.756 Å / Total num. of bins used: 20
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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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