+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29071 | ||||||||||||
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Title | TFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene | ||||||||||||
Map data | Main map postprocessed in Relion | ||||||||||||
Sample |
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Keywords | transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||||||||
Function / homology | Function and homology information RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III core binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation ...RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III core binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA 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 / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / phosphatase activity / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / DNA-templated transcription initiation / disordered domain specific binding / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Talyzina A / He Y | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: bioRxiv / 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 cryo-electron microscopy to visualize the complex of TFIIIA and TFIIIC bound to the promoter. Brf1-TBP binding further stabilizes the DNA, resulting in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA 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 mechanism of how the transcription initiation complex assembles on the 5S rRNA promoter, a crucial step in Pol III transcription regulation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29071.map.gz | 202.5 MB | EMDB map data format | |
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Header (meta data) | emd-29071-v30.xml emd-29071.xml | 38.3 KB 38.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29071_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_29071.png | 97.3 KB | ||
Others | emd_29071_additional_1.map.gz emd_29071_additional_2.map.gz emd_29071_half_map_1.map.gz emd_29071_half_map_2.map.gz | 149.7 MB 145.3 MB 171.2 MB 171.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29071 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29071 | HTTPS FTP |
-Validation report
Summary document | emd_29071_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_29071_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_29071_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | emd_29071_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29071 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29071 | HTTPS FTP |
-Related structure data
Related structure data | 8ffzMC 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_29071.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main map postprocessed in Relion | ||||||||||||||||||||
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: Main map postprocessed with deepEMhancer
File | emd_29071_additional_1.map | ||||||||||||
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Annotation | Main map postprocessed with deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refinement of Brf1-TBP-tau131-DNA, postprocessed with deepEMhancer...
File | emd_29071_additional_2.map | ||||||||||||
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Annotation | Focused refinement of Brf1-TBP-tau131-DNA, postprocessed with deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 of main map
File | emd_29071_half_map_1.map | ||||||||||||
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Annotation | Half1 of main map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 of main map
File | emd_29071_half_map_2.map | ||||||||||||
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Annotation | Half2 of main map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene
+Supramolecule #1: TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene
+Macromolecule #1: Transcription factor IIIA
+Macromolecule #2: Transcription factor tau 138 kDa subunit
+Macromolecule #3: Transcription factor tau 131 kDa subunit
+Macromolecule #4: Transcription factor tau 95 kDa subunit
+Macromolecule #5: Transcription factor tau 91 kDa subunit
+Macromolecule #6: Transcription factor tau 60 kDa subunit
+Macromolecule #7: Transcription factor tau 55 kDa subunit
+Macromolecule #8: Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein
+Macromolecule #9: DNA (151-MER)
+Macromolecule #10: DNA (151-MER)
+Macromolecule #11: ZINC ION
-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 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR |
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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Output model | PDB-8ffz: |