+Open data
-Basic information
Entry | Database: PDB / ID: 8hsh | |||||||||
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Title | Thermus thermophilus RNA polymerase coreenzyme | |||||||||
Components | (DNA-directed RNA polymerase subunit ...) x 4 | |||||||||
Keywords | TRANSCRIPTION / RNA polymerase coreenzyme | |||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Murayama, Y. / Ehara, H. / Sekine, S. | |||||||||
Funding support | Japan, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hsh.cif.gz | 537.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hsh.ent.gz | 419.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hsh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hsh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8hsh_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8hsh_validation.xml.gz | 87.9 KB | Display | |
Data in CIF | 8hsh_validation.cif.gz | 131.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/8hsh ftp://data.pdbj.org/pub/pdb/validation_reports/hs/8hsh | HTTPS FTP |
-Related structure data
Related structure data | 34997MC 8hsgC 8hsjC 8hslC 8hsrC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules GHIJK
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpoA, TTHA1664 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHR6, DNA-directed RNA polymerase #2: Protein | | Mass: 125436.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpoB, TTHA1813 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | | Mass: 171994.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpoC, TTHA1812 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase #4: Protein | | Mass: 11491.237 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpoZ, TTHA1561 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RQE7, DNA-directed RNA polymerase |
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-Non-polymers , 2 types, 3 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RNA polymerase coreenzyme / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 392560 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 169.62 Å2 | ||||||||||||||||||||||||
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