+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26547 | |||||||||
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Title | Mediator-PIC Early (Tail A + Upstream DNA & Activator) | |||||||||
Map data | Mediator-PIC Early (Tail A Upstream DNA) | |||||||||
Sample |
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Keywords | Divergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16 / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information regulation of transcription from RNA polymerase II promoter by galactose / TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / galactose metabolic process / core mediator complex / mediator complex / positive regulation of transcription from RNA polymerase II promoter by galactose / TFIIB-class transcription factor binding ...regulation of transcription from RNA polymerase II promoter by galactose / TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / galactose metabolic process / core mediator complex / mediator complex / positive regulation of transcription from RNA polymerase II promoter by galactose / TFIIB-class transcription factor binding / replicative senescence / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / transcription repressor complex / response to endoplasmic reticulum stress / cellular response to heat / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Gorbea Colon JJ / Chen S-F / Tsai KL / Murakami K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural basis of a transcription pre-initiation complex on a divergent promoter. Authors: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami / Abstract: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26547.map.gz | 40.1 MB | EMDB map data format | |
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Header (meta data) | emd-26547-v30.xml emd-26547.xml | 27.1 KB 27.1 KB | Display Display | EMDB header |
Images | emd_26547.png | 39.7 KB | ||
Masks | emd_26547_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-26547.cif.gz | 9.1 KB | ||
Others | emd_26547_half_map_1.map.gz emd_26547_half_map_2.map.gz | 40.5 MB 40.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26547 | HTTPS FTP |
-Validation report
Summary document | emd_26547_validation.pdf.gz | 678.8 KB | Display | EMDB validaton report |
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Full document | emd_26547_full_validation.pdf.gz | 678.4 KB | Display | |
Data in XML | emd_26547_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_26547_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26547 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26547 | HTTPS FTP |
-Related structure data
Related structure data | 7uikMC 7ui9C 7uicC 7uifC 7uigC 7uilC 7uioC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26547.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Mediator-PIC Early (Tail A Upstream DNA) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26547_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_26547_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_26547_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Med-PICEarly (TailA+Activator & DNA Class 1)
+Supramolecule #1: Med-PICEarly (TailA+Activator & DNA Class 1)
+Macromolecule #1: DNA (38-MER)
+Macromolecule #2: DNA (37-MER)
+Macromolecule #3: Regulatory protein GAL4
+Macromolecule #4: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #5: Mediator of RNA polymerase II transcription subunit 2
+Macromolecule #6: Mediator of RNA polymerase II transcription subunit 3
+Macromolecule #7: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #8: Mediator of RNA polymerase II transcription subunit 5
+Macromolecule #9: Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .1 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 40900 / Average exposure time: 3.4 sec. / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199834 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |