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- PDB-8rao: Structure of Sen1-ADP.BeF3-RNA complex -

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Basic information

Entry
Database: PDB / ID: 8rao
TitleStructure of Sen1-ADP.BeF3-RNA complex
Components
  • Helicase SEN1
  • RNA
KeywordsGENE REGULATION / RNA Polymerase II / Pol II / termination / Sen1
Function / homology
Function and homology information


negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / transcription termination site sequence-specific DNA binding / Nrd1 complex / sno(s)RNA 3'-end processing / DNA-templated DNA replication maintenance of fidelity / snRNA processing / mRNA 3'-end processing / tRNA processing / termination of RNA polymerase II transcription ...negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / transcription termination site sequence-specific DNA binding / Nrd1 complex / sno(s)RNA 3'-end processing / DNA-templated DNA replication maintenance of fidelity / snRNA processing / mRNA 3'-end processing / tRNA processing / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / transcription-coupled nucleotide-excision repair / cell redox homeostasis / replication fork / maturation of SSU-rRNA / small-subunit processome / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / 5'-3' DNA helicase activity / hydrolase activity / nuclear body / protein domain specific binding / mRNA binding / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / : / SEN1 N terminal / Helicase SEN1 beta-barrel domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal ...Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / : / SEN1 N terminal / Helicase SEN1 beta-barrel domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / RNA (> 10) / Helicase SEN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Human immunodeficiency virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsRengachari, S. / Lidscreiber, M. / Cramer, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mechanism of polyadenylation-independent RNA polymerase II termination.
Authors: Srinivasan Rengachari / Thomas Hainthaler / Christiane Oberthuer / Michael Lidschreiber / Patrick Cramer /
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 ...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.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Feb 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Helicase SEN1
P: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,6365
Polymers264,1192
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3660 Å2
ΔGint-28 kcal/mol
Surface area30810 Å2
MethodPISA

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Components

#1: Protein Helicase SEN1


Mass: 252835.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEN1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00416
#2: RNA chain RNA


Mass: 11282.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Sen1-ADP.BeF3-RNA complexCOMPLEX#1-#20MULTIPLE SOURCES
2Helicase SEN1COMPLEX#11RECOMBINANT
3RNACOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (brewer's yeast)4932
33Human immunodeficiency virus 211709
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Trichoplusia ni (cabbage looper)7111
43synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40.02 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15633 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16I59

6i59

16I592PDBexperimental model
22XZO

2xzo

12XZO3PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0015904
ELECTRON MICROSCOPYf_angle_d0.4068002
ELECTRON MICROSCOPYf_dihedral_angle_d13.3092289
ELECTRON MICROSCOPYf_chiral_restr0.038887
ELECTRON MICROSCOPYf_plane_restr0.002997

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