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Open data
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Basic information
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Title | Structure of EC+EC (leading EC-focused) | |||||||||
![]() | Leading EC_map_with_sharpening by postprocesssed in Relion | |||||||||
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Function / homology | ![]() : / : / RNA polymerase III activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex ...: / : / RNA polymerase III activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translation initiation factor binding / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / DNA-templated transcription / nucleotide binding / nucleolus / DNA binding / zinc ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
![]() | Yang C / Murakami K | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami / ![]() Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34.2 KB 34.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.9 KB | Display | ![]() |
Images | ![]() | 67.9 KB | ||
Masks | ![]() | 40.6 MB | ![]() | |
Others | ![]() ![]() ![]() | 31.2 MB 31.3 MB 31.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 871.9 KB | Display | ![]() |
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Full document | ![]() | 871.4 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mkaMC ![]() 7meiC ![]() 7mk9C ![]() 7ml0C ![]() 7ml1C ![]() 7ml2C ![]() 7ml3C ![]() 7ml4C 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
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Annotation | Leading EC_map_with_sharpening by postprocesssed in Relion | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Leading EC map without sharpening
File | emd_23888_additional_1.map | ||||||||||||
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Annotation | Leading EC_map_without_sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EC+EC (leading EC-focused) half map 1
File | emd_23888_half_map_1.map | ||||||||||||
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Annotation | EC+EC (leading EC-focused) half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EC+EC (leading EC-focused) half map 2
File | emd_23888_half_map_2.map | ||||||||||||
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Annotation | EC+EC (leading EC-focused) half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : The leading EC of complex EC+EC
+Supramolecule #1: The leading EC of complex EC+EC
+Macromolecule #1: DNA (40-MER)
+Macromolecule #2: DNA (40-MER)
+Macromolecule #3: DNA-directed RNA polymerase subunit
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #6: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #8: DNA-directed RNA polymerases I,II,and III subunit RPABC2
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #12: DNA-directed RNA polymerases II subunit RPABC5
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #14: DNA-directed RNA polymerases II subunit RPABC4
+Macromolecule #15: RNA (5'-R(P*AP*AP*CP*UP*AP*GP*UP*UP*AP*AP*GP*AP*GP*GP*UP*U)-3')
+Macromolecule #16: ZINC ION
+Macromolecule #17: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.6 / Details: 20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
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 (6k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 81000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |