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Yorodumi- EMDB-29356: Focused refinement on the Brf1-TBP-DNA within TFIIIA-TFIIIC-Brf1-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29356 | ||||||||||||
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Title | Focused refinement on the Brf1-TBP-DNA within TFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene | ||||||||||||
Map data | postprocessed map | ||||||||||||
Sample |
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Keywords | transcription factor / TRANSCRIPTION-DNA complex | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.14 Å | ||||||||||||
Authors | Talyzina A / He Y | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Authors: Anna Talyzina / Yan Han / Chiranjib Banerjee / Susan Fishbain / Alexis Reyes / Reza Vafabakhsh / Yuan He / Abstract: RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors ...RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here, we use cryoelectron microscopy (cryo-EM) to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Gene-specific factor TFIIIA interacts with DNA and acts as an adaptor for TFIIIC-promoter interactions. We also visualize DNA binding of TFIIIB subunits, Brf1 and TBP (TATA-box binding protein), which results in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA within the complex undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the transcription initiation complex assembly on the 5S rRNA promoter and allow us to directly compare Pol III and Pol II transcription adaptations. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29356.map.gz | 106.2 MB | EMDB map data format | |
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Header (meta data) | emd-29356-v30.xml emd-29356.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_29356.png | 24 KB | ||
Others | emd_29356_additional_1.map.gz emd_29356_half_map_1.map.gz emd_29356_half_map_2.map.gz | 145.3 MB 200.4 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29356 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29356 | HTTPS FTP |
-Validation report
Summary document | emd_29356_validation.pdf.gz | 935.4 KB | Display | EMDB validaton report |
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Full document | emd_29356_full_validation.pdf.gz | 935 KB | Display | |
Data in XML | emd_29356_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_29356_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29356 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29356 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29356.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | postprocessed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: deepemhancer map
File | emd_29356_additional_1.map | ||||||||||||
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Annotation | deepemhancer map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 2
File | emd_29356_half_map_1.map | ||||||||||||
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Annotation | half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 1
File | emd_29356_half_map_2.map | ||||||||||||
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Annotation | half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene
Entire | Name: TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene |
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Components |
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-Supramolecule #1: TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene
Supramolecule | Name: TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 810 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: Quantifoil R2/1 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm |
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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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