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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Mediator-PIC Early (Composite Model) | |||||||||
![]() | composite map of Med-PICearly | |||||||||
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![]() | Divergent transcription / Mediator / ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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
Supplemental images |
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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 |
-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 | ![]() |
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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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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![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
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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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: PROJECTION MATCHING |
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 |
-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: |