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- EMDB-19021: Structure of Sen1-ADP.BeF3-RNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19021
TitleStructure of Sen1-ADP.BeF3-RNA complex
Map data
Sample
  • Complex: Sen1-ADP.BeF3-RNA complex
    • Complex: Helicase SEN1
      • Protein or peptide: Helicase SEN1
    • Complex: RNA
      • RNA: RNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsRNA Polymerase II / Pol II / termination / Sen1 / GENE REGULATION
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Human immunodeficiency virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsRengachari S / Lidscreiber M / Cramer P
Funding support Germany, 1 items
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, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19021.png

Downloads & links

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Map

FileDownload / File: emd_19021.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.035642017 - 0.082285106
Average (Standard dev.)-0.00033619575 (±0.0016082026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19021_msk_1.map
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Half map: #1

Fileemd_19021_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19021_half_map_2.map
Projections & Slices
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Sample components

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Entire : Sen1-ADP.BeF3-RNA complex

EntireName: Sen1-ADP.BeF3-RNA complex
Components
  • Complex: Sen1-ADP.BeF3-RNA complex
    • Complex: Helicase SEN1
      • Protein or peptide: Helicase SEN1
    • Complex: RNA
      • RNA: RNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Sen1-ADP.BeF3-RNA complex

SupramoleculeName: Sen1-ADP.BeF3-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Helicase SEN1

SupramoleculeName: Helicase SEN1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 2

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Macromolecule #1: Helicase SEN1

MacromoleculeName: Helicase SEN1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 252.835922 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNSNNPDNNN SNNINNNNKD KDIAPNSDVQ LATVYTKAKS YIPQIEQVYQ GTNPNIQEAK LLGELLQVLA EVPKGTHLFC DPILEPISI FSLTIFSFNE EATATWLKNH FNPILSVCDK CILNFARGKC KMLQHFAIQR HVPHEHVAKF NDIVCQWRVE A VFPILRNI ...String:
MNSNNPDNNN SNNINNNNKD KDIAPNSDVQ LATVYTKAKS YIPQIEQVYQ GTNPNIQEAK LLGELLQVLA EVPKGTHLFC DPILEPISI FSLTIFSFNE EATATWLKNH FNPILSVCDK CILNFARGKC KMLQHFAIQR HVPHEHVAKF NDIVCQWRVE A VFPILRNI SVNDNTGINI TNEIETAMYE CLCNPHMLRL NKQLKATFEA IFKFFYDTKH RLLDVTNPLS IKTFISGVIF CW CEGSKEE NEWSRAFLKD LYSRNFHINL SNLTPDIIEE VYIHILFLQN PANWTEIVVS QFWSRLLPVF NLFDKDVFIE YFQ VPKNVE SLKKTFKFPL EPIFKMWYNH LSKSYHDKPL DFLLRGLTMF LNKFGSEFWS KIEPFTFHSI LDIIFNRDSF PIKL IKIQD NPIVEHQTEV YFQLTGSVTD LLSWTLPFYH ALSPSKRIQM VRKVSMAFLR IIANYPSLKS IPKACLMNSA TALLR AVLT IKENERAMLY KNDEFETVLL TKTDSRALLN NPLIQDIIIR SASNPNDFYP GLGAASASVA TSTMMVLAEC IDFDIL LLC HRTFKLYSGK PISEIPISTN VLENVTNKID LRSFHDGPLL AKQLLVSLKN INGLLIVPSN TAVAEAHNAL NQKFLLL ST RLMEKFADIL PGQLSKILAD EDASQGFWSC IFSSDKHLYQ AATNILYNTF DVEGRLEGIL AILNSNLTVN LKNINVML Q RLINCEFYEP CPRAVRVLMD VVSAFVDPIS GVFANFQTLK SQNTEKEFLK FWESCWLFLD TIYKFTLKWA SKYDYSELE NFTKDTLDLS RSLVDSFREF SDILHDQTKN LLLNVLETFK NMLYWLRLSD EVLLESCVRL IISTSDLAHE KHVKVDDSLV EMMAKYASK AKRFSNKLTE QQASEILQKA KIFNKALTEE VATEAENYRK EKELSRLGKV IDLTDSVPAS PSLSPSLSST I ASSSAESR ADYLQRKALS SSITGRPRVA QPKITSFGTF QSSANAKLHR TKPVKPLSKM ELARMQLLNN RVVHPPSAPA FH TKSRGLS NKNDDSSSEE SDNDIESARE LFAIAKAKGK GIQTVDINGK VVKRQTAAEL AKQELEHMRK RLNVDMNPLY EII LQWDYT RNSEYPDDEP IGNYSDVKDF FNSPADYQKV MKPLLLLESW QGLCSSRDRE DYKPFSIIVG NRTAVSDFYD VYAS VAKQV IQDCGISESD LIVMAYLPDF RPDKRLSSDD FKKAQHTCLA KVRTLKNTKG GNVDVTLRIH RNHSFSKFLT LRSEI YCVK VMQMTTIERE YSTLEGLEYY DLVGQILQAK PSPPVNVDAA EIETVKKSYK LNTSQAEAIV NSVSKEGFSL IQGPPG TGK TKTILGIIGY FLSTKNASSS NVIKVPLEKN SSNTEQLLKK QKILICAPSN AAVDEICLRL KSGVYDKQGH QFKPQLV RV GRSDVVNVAI KDLTLEELVD KRIGERNYEI RTDPELERKF NNAVTKRREL RGKLDSESGN PESPMSTEDI SKLQLKIR E LSKIINELGR DRDEMREKNS VNYRNRDLDR RNAQAHILAV SDIICSTLSG SAHDVLATMG IKFDTVIIDE ACQCTELSS IIPLRYGGKR CIMVGDPNQL PPTVLSGAAS NFKYNQSLFV RMEKNSSPYL LDVQYRMHPS ISKFPSSEFY QGRLKDGPGM DILNKRPWH QLEPLAPYKF FDIISGRQEQ NAKTMSYTNM EEIRVAIELV DYLFRKFDNK IDFTGKIGII SPYREQMQKM R KEFARYFG GMINKSIDFN TIDGFQGQEK EIILISCVRA DDTKSSVGFL KDFRRMNVAL TRAKTSIWVL GHQRSLAKSK LW RDLIEDA KDRSCLAYAC SGFLDPRNNR AQSILRKFNV PVPSEQEDDY KLPMEYITQG PDEVKSNKDT KKRRVVDEGE EAD KAVKKK KKEKKKEKKK SKADDKKKNN KKAESPSTSS GTKKKSSIFG GMSVPSAVVP KTFPDVDSNK KAAAVVGKKK NNKH VCFSD DVSFIPRNDE PEIKVTRSLS SVLKEKQLGL KETRTISPPE ISNNEDDDDE DDYTPSISDS SLMKSEANGR NNRVA SHNQ NFSASIYDDP QVSQAKQTQV PAAITKHRSS NSVLSGGSSR ILTASDYGEP NQNGQNGANR TLSQHVGNAN QYSTAP VGT GELHETLPAH PQDSYPAEAE DPYDLNPHPQ PQSSAFKGPG SGPTGTRNSS RRNASSSPFI PKKRKPRS

UniProtKB: Helicase SEN1

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 11.28279 KDa
SequenceString:
AGUCGUGCGU CUAAUAACCG GAGAGGGAAC CCACU

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15633
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6i59

source_name: PDB, initial_model_type: experimental model

2xzo

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: OTHER
Output model

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

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