+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2634 | |||||||||
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Title | Electron cryo-microscopy of yeast transcriptional Mediator | |||||||||
Map data | Reconstruction of yeast transcriptional Mediator | |||||||||
Sample |
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Keywords | transcription / mediator / Srb / RNAPII / regulation / activator | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Tsai KL / Tomomori-Sato C / Sato S / Conaway RC / Conaway JW / Asturias FJ | |||||||||
Citation | Journal: Cell / Year: 2014 Title: Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Authors: Kuang-Lei Tsai / Chieri Tomomori-Sato / Shigeo Sato / Ronald C Conaway / Joan W Conaway / Francisco J Asturias / Abstract: The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA ...The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA polymerase II (RNAPII) transcription machinery. Efforts to uncover the Mediator mechanism have been hindered by a poor understanding of its structure, subunit organization, and conformational rearrangements. By overcoming biochemical and image analysis hurdles, we obtained accurate EM structures of yeast and human Mediators. Subunit localization experiments, docking of partial X-ray structures, and biochemical analyses resulted in comprehensive mapping of yeast Mediator subunits and a complete reinterpretation of our previous Mediator organization model. Large-scale Mediator rearrangements depend on changes at the interfaces between previously described Mediator modules, which appear to be facilitated by factors conducive to transcription initiation. Conservation across eukaryotes of Mediator structure, subunit organization, and RNA polymerase II interaction suggest conservation of fundamental aspects of the Mediator mechanism. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2634.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-2634-v30.xml emd-2634.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | EMD-2634_yMED.jpg | 60.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2634 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2634 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2634.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of yeast transcriptional Mediator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : yeast transcriptional Mediator
Entire | Name: yeast transcriptional Mediator |
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Components |
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-Supramolecule #1000: yeast transcriptional Mediator
Supramolecule | Name: yeast transcriptional Mediator / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: Mediator
Macromolecule | Name: Mediator / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S228C |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Date | Aug 18, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) Details: Every image is the average of 25 frames recorded by the direct electron detector |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2/SPARX / Number images used: 13006 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |