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Yorodumi- EMDB-36745: Thermus thermophilus Rho-engaged RNAP elongation complex; Rho part -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36745 | |||||||||
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Title | Thermus thermophilus Rho-engaged RNAP elongation complex; Rho part | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transcription elongation complex / Transcription termination / TRANSCRIPTION | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Murayama Y / Ehara H / Sekine S | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from . Authors: Yuko Murayama / Haruhiko Ehara / Mari Aoki / Mie Goto / Takeshi Yokoyama / Shun-Ichi Sekine / Abstract: Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the ...Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate-dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo-electron microscopy structure of the RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36745.map.gz | 40.7 MB | EMDB map data format | |
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Header (meta data) | emd-36745-v30.xml emd-36745.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_36745.png | 86 KB | ||
Others | emd_36745_half_map_1.map.gz emd_36745_half_map_2.map.gz | 40.8 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36745 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36745 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36745.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36745_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36745_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rho-engaged RNA polymerase elongation complex; Rho part
Entire | Name: Rho-engaged RNA polymerase elongation complex; Rho part |
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Components |
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-Supramolecule #1: Rho-engaged RNA polymerase elongation complex; Rho part
Supramolecule | Name: Rho-engaged RNA polymerase elongation complex; Rho part type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43245 |