PDB-8hsr: Thermus thermophilus Rho-engaged RNAP elongation complex (composi...

Basic information

• Entry: Database: PDB / ID: 8hsr
• Title: Thermus thermophilus Rho-engaged RNAP elongation complex (composite structure)

Components

• (DNA-directed RNA polymerase subunit ...) x 4
• DNA (31-MER)
• DNA (41-MER)
• RNA (29-MER)
• Transcription termination factor Rho

• Keywords: TRANSCRIPTION / Transcription elongation complex / Transcription termination

Function / homology

Function:

ATP-dependent activity, acting on RNA / DNA-directed RNA polymerase complex / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / cytoplasm

Domain/homology:

Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / : / DNA-directed RNA polymerase subunit beta', hybrid domain / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase

Component:

ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / RNA (> 100) / DNA-directed RNA polymerase subunit alpha / Transcription termination factor Rho / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta

• Biological species: Thermus thermophilus HB8 (bacteria); synthetic construct (others)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
• Authors: Murayama, Y. / Ehara, H. / Sekine, S.

Funding support

Japan, 2items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP17K15082	Japan
Japan Society for the Promotion of Science (JSPS)	JP20H05690	Japan

• 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 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

Deposition	Dec 20, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond / em_admin / struct Item: _em_admin.last_update / _em_admin.title / _struct.title