8RAO | pdb_00008rao

Experimental Data Snapshot

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wwPDB Validation 3D Report Full Report

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(2025) Nat Struct Mol Biol 32: 339-345

PubMed Abstract:
The mechanisms underlying the initiation and elongation of RNA polymerase II (Pol II) transcription are well-studied, whereas termination remains poorly understood. Here we analyze the mechanism of polyadenylation-independent Pol II termination mediated by the yeast Sen1 helicase. Cryo-electron microscopy structures of two pretermination intermediates show that Sen1 binds to Pol II and uses its adenosine triphosphatase activity to pull on exiting RNA in the 5' direction. This is predicted to push Pol II forward, induce an unstable hypertranslocated state and destabilize the transcription bubble, thereby facilitating termination. This mechanism of transcription termination may be widely used because it is conceptually conserved in the bacterial transcription system.

Organizational Affiliation

Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. srinivasan.rengachari@mpinat.mpg.de.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase SEN1	A [auth O]	2,231	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SEN1 EC: 3.6.4.13 (UniProt), 3.6.4.12 (UniProt)
UniProt
Find proteins for Q00416 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00416 Go to UniProtKB: Q00416
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00416
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
RNA	B [auth P]	35	Human immunodeficiency virus 2
Sequence Annotations Expand
Reference Sequence

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth O] MOL2 format, chain C [auth O] mmCIF format, chain C [auth O]	C [auth O]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth O] Interactions & Density Focus chain C [auth O]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain E [auth O] MOL2 format, chain E [auth O] mmCIF format, chain E [auth O]	E [auth O]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain E [auth O] Interactions & Density Focus chain E [auth O]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth O] MOL2 format, chain D [auth O] mmCIF format, chain D [auth O]	D [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth O] Interactions & Density Focus chain D [auth O]