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Yorodumi- PDB-8ram: Structure of Sen1 bound RNA Polymerase II pre-termination complex -
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Open data
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Basic information
| Entry | Database: PDB / ID: 8ram | |||||||||||||||||||||||||||
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| Title | Structure of Sen1 bound RNA Polymerase II pre-termination complex | |||||||||||||||||||||||||||
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Keywords | GENE REGULATION / RNA Polymerase II / Pol II / termination / Sen1 | |||||||||||||||||||||||||||
| Function / homology | Function and homology informationnegative regulation of flocculation / transcription termination site sequence-specific DNA binding / Nrd1 complex / 5'-3' DNA/RNA helicase activity / DNA/RNA helicase activity / DNA-templated DNA replication maintenance of fidelity / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA 3'-end processing / positive regulation of transcription elongation by RNA polymerase I / mating-type region heterochromatin ...negative regulation of flocculation / transcription termination site sequence-specific DNA binding / Nrd1 complex / 5'-3' DNA/RNA helicase activity / DNA/RNA helicase activity / DNA-templated DNA replication maintenance of fidelity / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA 3'-end processing / positive regulation of transcription elongation by RNA polymerase I / mating-type region heterochromatin / regulation of transcription-coupled nucleotide-excision repair / R-loop processing / RNA polymerase I core binding / RNA polymerase I general transcription initiation factor binding / snRNA processing / double-strand break repair involved in meiotic recombination / DSIF complex / premeiotic DNA replication / regulation of rRNA processing / intracellular mRNA localization / rDNA heterochromatin / rDNA binding / snRNP binding / U4 snRNA binding / transcription elongation factor complex / tRNA processing / mRNA 3'-end processing / DNA 5'-3' helicase / transcription elongation-coupled chromatin remodeling / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / spliceosomal complex assembly / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / termination of RNA polymerase II transcription / U2 snRNA binding / U5 snRNA binding / 7-methylguanosine mRNA capping / termination of RNA polymerase I transcription / Dual incision in TC-NER / U1 snRNA binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / U6 snRNA binding / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase III / nuclear-transcribed mRNA catabolic process / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / cell redox homeostasis / positive regulation of autophagy / transcription-coupled nucleotide-excision repair / translesion synthesis / translation initiation factor binding / negative regulation of autophagy / replication fork / transcription initiation-coupled chromatin remodeling / DNA-templated transcription elongation / positive regulation of transcription elongation by RNA polymerase II / DNA-templated transcription initiation / P-body / transcription initiation at RNA polymerase II promoter / DNA-templated transcription termination / mRNA processing / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / transcription by RNA polymerase II / kinetochore / ribonucleoside binding / cytoplasmic stress granule / DNA-directed RNA polymerase / rRNA processing / DNA-directed RNA polymerase activity / peroxisome / single-stranded DNA binding Similarity search - Function | |||||||||||||||||||||||||||
| Biological species | ![]() Human immunodeficiency virus 2 | |||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||||||||||||||
Authors | Rengachari, S. / Lidscreiber, M. / Cramer, P. | |||||||||||||||||||||||||||
| Funding support | Germany, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: 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. | |||||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8ram.cif.gz | 1021.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb8ram.ent.gz | 785.8 KB | Display | PDB format |
| PDBx/mmJSON format | 8ram.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/8ram ftp://data.pdbj.org/pub/pdb/validation_reports/ra/8ram | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 19019MC ![]() 8ranC ![]() 8raoC ![]() 8rapC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK
| #1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
| #5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Transcription elongation factor ... , 3 types, 3 molecules MYZ
| #13: Protein | Mass: 16179.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ELF1, YKL160W, YKL614 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36053 |
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| #18: Protein | Mass: 11168.772 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SPT4, YGR063C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32914 |
| #19: Protein | Mass: 115797.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SPT5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27692 |
-DNA chain , 2 types, 2 molecules NT
| #14: DNA chain | Mass: 17793.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 2 |
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| #17: DNA chain | Mass: 18009.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 2 |
-Protein / RNA chain , 2 types, 2 molecules OP
| #15: Protein | Mass: 252835.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SEN1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00416 |
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| #16: RNA chain | Mass: 11282.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 2 |
-Non-polymers , 2 types, 10 molecules 


| #20: Chemical | ChemComp-ZN / #21: Chemical | ChemComp-MG / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | N |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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| Source (natural) |
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| Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TITAN KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
| Image recording | Electron dose: 40.02 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
| EM software | Name: PHENIX / Category: model refinement | |||||||||||||||||||||||||||||||||||
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95644 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: OTHER | |||||||||||||||||||||||||||||||||||
| Atomic model building |
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| Refine LS restraints |
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About Yorodumi




Human immunodeficiency virus 2
Germany, 1items
Citation






PDBj


































































Trichoplusia ni (cabbage looper)
FIELD EMISSION GUN


