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Open data
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Basic information
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Title | Mediator-PIC Early (Composite Model) | |||||||||
![]() | composite map of Med-PICearly | |||||||||
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![]() | Divergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16 / TRANSCRIPTION | |||||||||
Function / homology | ![]() regulation of transcription from RNA polymerase II promoter by galactose / TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / galactose metabolic process / mRNA cleavage and polyadenylation specificity factor complex / core mediator complex ...regulation of transcription from RNA polymerase II promoter by galactose / TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / galactose metabolic process / mRNA cleavage and polyadenylation specificity factor complex / 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 / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / mediator complex / positive regulation of transcription from RNA polymerase II promoter by galactose / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / 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 / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / TFIID-class transcription factor complex binding / Estrogen-dependent gene expression / transcription by RNA polymerase III / acetyltransferase activity / TFIIB-class transcription factor binding / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / transcription repressor complex / transcription antitermination / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / transcription corepressor activity / peroxisome / ribosome biogenesis / protein-macromolecule adaptor activity / single-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA recombination / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Gorbea Colon JJ / Chen S-F / Tsai KL / Murakami K | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Downloads & links
-EMDB archive
Map data | ![]() | 36.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 63.5 KB 63.5 KB | Display Display | ![]() |
Images | ![]() | 96.8 KB | ||
Filedesc metadata | ![]() | 17.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 337.9 KB | Display | ![]() |
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Full document | ![]() | 337.5 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uioMC ![]() 7ui9C ![]() 7uicC ![]() 7uifC ![]() 7uigC ![]() 7uikC ![]() 7uilC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | composite map of Med-PICearly | ||||||||||||||||||||
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
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Sample components
+Entire : Med-PICearly
+Supramolecule #1: Med-PICearly
+Macromolecule #1: DNA (38-MER)
+Macromolecule #2: DNA (37-MER)
+Macromolecule #3: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #4: Mediator of RNA polymerase II transcription subunit 2
+Macromolecule #5: Mediator of RNA polymerase II transcription subunit 3
+Macromolecule #6: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #7: Mediator of RNA polymerase II transcription subunit 5
+Macromolecule #8: Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #9: Regulatory protein GAL4
+Macromolecule #10: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #11: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #12: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #13: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #14: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #15: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #16: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #17: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #18: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #19: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #20: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #21: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #22: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #23: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #24: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #25: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #26: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #27: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #28: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #29: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #30: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #31: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #32: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #33: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #34: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #35: Transcription initiation factor IIB
+Macromolecule #36: Transcription initiation factor IIF subunit alpha
+Macromolecule #37: Transcription initiation factor IIF subunit beta
+Macromolecule #38: Transcription elongation factor S-II
+Macromolecule #39: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #40: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #41: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #42: ZINC ION
+Macromolecule #43: THREONINE
+Macromolecule #44: ALANINE
+Macromolecule #45: ASPARTIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: Quantifoil / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.4 sec. / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Number classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1102984 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation | ||||||||
Output model | ![]() PDB-7uio: |