8RAM image
Deposition Date 2023-12-01
Release Date 2024-10-30
Last Version Date 2025-07-02
Entry Detail
PDB ID:
8RAM
Keywords:
GENE REGULATION
Title:
Structure of Sen1 bound RNA Polymerase II pre-termination complex
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Human immunodeficiency virus 2 (Taxon ID: 11709)
Host Organism:
Trichoplusia ni
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8RAM validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04050 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:1224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P16370 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20433 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20434 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20435 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P34087 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20436 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P27999 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22139 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38902 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40422 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor 1
Gene (Uniprot):ELF1
Chain IDs:M
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36053 Pfam ID:PF05129
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template strand
Chain IDs:N
Chain Length:58
Number of Molecules:1
Biological Source:Human immunodeficiency virus 2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Helicase SEN1
Gene (Uniprot):SEN1
Chain IDs:O
Chain Length:2231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q00416 Pfam ID:PF12726, PF13086, PF13087 EC:3.6.4.12
Polymer Type:polyribonucleotide
Molecule:RNA
Chain IDs:P
Chain Length:35
Number of Molecules:1
Biological Source:Human immunodeficiency virus 2
Polymer Type:polydeoxyribonucleotide
Molecule:Template strand
Chain IDs:Q (auth: T)
Chain Length:58
Number of Molecules:1
Biological Source:Human immunodeficiency virus 2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):SPT4
Chain IDs:R (auth: Y)
Chain Length:102
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32914 Pfam ID:PF06093
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT5
Gene (Uniprot):SPT5
Chain IDs:S (auth: Z)
Chain Length:1063
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P27692 Pfam ID:PF11942, PF03439, PF00467, PF12815
Ligand Molecules
MG
ZN
Primary Citation
Mechanism of polyadenylation-independent RNA polymerase II termination.
Nat.Struct.Mol.Biol. 32 339 345 (2025)
PMID: 39424994 DOI: 10.1038/s41594-024-01409-0

Abstact

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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Primary Citation of related structures
8RAM