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- PDB-4h62: Structure of the Saccharomyces cerevisiae Mediator subcomplex Med... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h62 | ||||||
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Title | Structure of the Saccharomyces cerevisiae Mediator subcomplex Med17C/Med11C/Med22C | ||||||
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![]() | TRANSCRIPTION / MEDIATOR COMPLEX / NUCLEUS | ||||||
Function / homology | ![]() RNA polymerase II complex recruiting activity / core mediator complex / TFIIH-class transcription factor complex binding / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity ...RNA polymerase II complex recruiting activity / core mediator complex / TFIIH-class transcription factor complex binding / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / DNA-binding transcription factor binding / transcription coactivator activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P. | ||||||
![]() | ![]() Title: Structure of the Mediator head module. Authors: Lariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.4 KB | Display | ![]() |
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PDB format | ![]() | 119.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.7 KB | Display | ![]() |
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Full document | ![]() | 472.8 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 4341.593 Da / Num. of mol.: 1 / Fragment: C-terminal region (Unp residues 84-115) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Gene: MED11, YM9718.11C, YMR112C / Plasmid: pET-28b / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 3404.732 Da / Num. of mol.: 1 / Fragment: C-terminal region (Unp residues 96-121) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Gene: MED22, SRB6, YBR1721, YBR253W / Plasmid: pET-28b / Production host: ![]() ![]() |
#3: Protein | Mass: 36552.348 Da / Num. of mol.: 1 / Fragment: C-terminal region (Unp residues 377-687) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Gene: MED17, SRB4, YER022W / Plasmid: pET-21b / Production host: ![]() ![]() |
#4: Chemical | ChemComp-MES / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, 4 M ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97972 Å / Relative weight: 1 |
Reflection | Resolution: 3→130.615 Å / Num. all: 24338 / Num. obs: 24338 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 16.46 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.6922 / Mean I/σ(I) obs: 0.56 / Rsym value: 0.6922 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 3→65.308 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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