+Open data
-Basic information
Entry | Database: PDB / ID: 1yke | ||||||
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Title | Structure of the mediator MED7/MED21 subcomplex | ||||||
Components |
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Keywords | GENE REGULATION | ||||||
Function / homology | Function and homology information core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of transcription by RNA polymerase II ...core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription corepressor activity / RNA polymerase II-specific 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Baumli, S. / Hoeppner, S. / Cramer, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. Authors: Baumli, S. / Hoeppner, S. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yke.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yke.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yke_validation.pdf.gz | 457.4 KB | Display | wwPDB validaton report |
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Full document | 1yke_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 1yke_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1yke_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1yke ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1yke | HTTPS FTP |
-Related structure data
-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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Details | the presumed biological unit consists of MED7 and MED21 as a heterodimer. |
-Components
#1: Protein | Mass: 12964.011 Da / Num. of mol.: 2 / Fragment: residues 102-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08278 #2: Protein | Mass: 17377.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P47822 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.37 Å3/Da / Density % sol: 77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: sodium chloride, PEG 6000, ethanol, b-mercaptoethanol, EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0749 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 23, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0749 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 20724 / Num. obs: 20641 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.3→3.42 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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