+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26542 | |||||||||
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Title | Core Mediator-PICearly (Copy A) | |||||||||
Map data | Core Mediator-PICearly (Copy A) - Unsharpened | |||||||||
Sample |
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Function / homology | Function and homology information meiotic gene conversion / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter ...meiotic gene conversion / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / mediator complex / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / TFIID-class transcription factor complex binding / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / TFIIB-class transcription factor binding / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / cellular response to nutrient levels / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / translation initiation factor binding / TBP-class protein binding / transcription antitermination / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / transcription corepressor activity / ribosome biogenesis / peroxisome / protein-macromolecule adaptor activity / single-stranded DNA binding / cellular response to heat / DNA-binding transcription factor binding / DNA recombination / transcription coactivator activity / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA repair / DNA-templated transcription / mRNA binding / nucleotide binding / regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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_26542.map.gz | 141 MB | EMDB map data format | |
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Header (meta data) | emd-26542-v30.xml emd-26542.xml | 58.6 KB 58.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26542_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_26542.png | 41.7 KB | ||
Masks | emd_26542_msk_1.map | 178 MB | Mask map | |
Others | emd_26542_additional_1.map.gz emd_26542_additional_2.map.gz emd_26542_half_map_1.map.gz emd_26542_half_map_2.map.gz | 10.8 MB 165.1 MB 140.9 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26542 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26542 | HTTPS FTP |
-Validation report
Summary document | emd_26542_validation.pdf.gz | 651.3 KB | Display | EMDB validaton report |
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Full document | emd_26542_full_validation.pdf.gz | 650.8 KB | Display | |
Data in XML | emd_26542_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_26542_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26542 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26542 | HTTPS FTP |
-Related structure data
Related structure data | 7ui9MC 7uicC 7uifC 7uigC 7uikC 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_26542.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Core Mediator-PICearly (Copy A) - Unsharpened | ||||||||||||||||||||
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_26542_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Core Mediator-PICearly (Copy A) - Sharpened (DeepEMhancer)
File | emd_26542_additional_1.map | ||||||||||||
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Annotation | Core Mediator-PICearly (Copy A) - Sharpened (DeepEMhancer) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Core Mediator-PICearly (Copy A) - Sharpened (Relion)
File | emd_26542_additional_2.map | ||||||||||||
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Annotation | Core Mediator-PICearly (Copy A) - Sharpened (Relion) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Core Mediator-PICearly (Copy A) - Half Map 1
File | emd_26542_half_map_1.map | ||||||||||||
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Annotation | Core Mediator-PICearly (Copy A) - Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Core Mediator-PICearly (Copy A) - Half Map 2
File | emd_26542_half_map_2.map | ||||||||||||
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Annotation | Core Mediator-PICearly (Copy A) - Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Core Mediator-PICearly (Copy A)
+Supramolecule #1: Core Mediator-PICearly (Copy A)
+Macromolecule #1: Transcription initiation factor IIB
+Macromolecule #2: Transcription initiation factor IIF subunit alpha
+Macromolecule #3: Transcription initiation factor IIF subunit beta
+Macromolecule #4: Transcription elongation factor S-II
+Macromolecule #5: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #6: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #7: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #8: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #9: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #10: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #11: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #12: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #13: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #14: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #15: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #16: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #17: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #18: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #19: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #20: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #21: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #22: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #23: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #24: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #25: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #26: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #27: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #28: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #29: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #30: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #31: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #32: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #33: DNA-directed RNA polymerases I, II, and III subunit RPABC4
-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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Grid | Model: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | |||||||||||||||
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 |