+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14450 | |||||||||
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Title | Pol III PTC - Full transcription bubble | |||||||||
Map data | Pol III PTC NTPs DNA/RNA classified Sharpened with LocalDeblur | |||||||||
Sample |
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Keywords | RNA synthesis / short RNAs / termination / TRANSCRIPTION | |||||||||
Biological species | Saccharomyces cerevisiae W303 (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Girbig M / Mueller CW | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Cell Rep / Year: 2022 Title: Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals. Authors: Mathias Girbig / Juanjuan Xie / Helga Grötsch / Domenico Libri / Odil Porrua / Christoph W Müller / Abstract: RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches ...RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches the termination signal, it pauses and forms the pre-termination complex (PTC). Here, we report cryoelectron microscopy (cryo-EM) structures of the yeast Pol III PTC and complementary functional states at resolutions of 2.7-3.9 Å. Pol III recognizes the poly(dT) termination signal with subunit C128 that forms a hydrogen-bond network with the NT strand and, thereby, induces pausing. Mutating key interacting residues interferes with transcription termination in vitro, impairs yeast growth, and causes global termination defects in vivo, confirming our structural results. Additional cryo-EM analysis reveals that C53-C37, a Pol III subcomplex and key termination factor, participates indirectly in Pol III termination. We propose a mechanistic model of Pol III transcription termination and rationalize why Pol III, unlike Pol I and Pol II, terminates on poly(dT) signals. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14450.map.gz | 152.8 MB | EMDB map data format | |
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Header (meta data) | emd-14450-v30.xml emd-14450.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14450_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_14450.png | 69.1 KB | ||
Filedesc metadata | emd-14450.cif.gz | 4.4 KB | ||
Others | emd_14450_additional_1.map.gz | 152.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14450 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14450 | HTTPS FTP |
-Validation report
Summary document | emd_14450_validation.pdf.gz | 460.4 KB | Display | EMDB validaton report |
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Full document | emd_14450_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | emd_14450_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_14450_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14450 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14450 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14450.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Pol III PTC NTPs DNA/RNA classified Sharpened with LocalDeblur | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Pol III PTC NTPs DNA/RNA classified Unsharpened map
File | emd_14450_additional_1.map | ||||||||||||
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Annotation | Pol III PTC NTPs DNA/RNA classified Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Yeast RNA Polymerase III PTC + NTPs, Full transcription bubble
Entire | Name: Yeast RNA Polymerase III PTC + NTPs, Full transcription bubble |
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Components |
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-Supramolecule #1: Yeast RNA Polymerase III PTC + NTPs, Full transcription bubble
Supramolecule | Name: Yeast RNA Polymerase III PTC + NTPs, Full transcription bubble type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20 |
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Source (natural) | Organism: Saccharomyces cerevisiae W303 (yeast) |
Molecular weight | Theoretical: 730 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.4 mg/mL | ||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 44.8 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: 2.25 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Protocol: OTHER |