8QEP image
Entry Detail
PDB ID:
8QEP
EMDB ID:
EMD-18375
Keywords:
TRANSCRIPTION
Title:
RNA polymerase II bound to Alu RNA right arm
Biological Source:
Source Organism:
Sus scrofa domesticus
PDB Version:
Deposition Date:
2023-09-01
Release Date:
2025-01-22
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8QEP validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit
Chain IDs:A
Chain Length:1970
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A8D1DPV6 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit beta
Chain IDs:B
Chain Length:1174
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A0B8RVL1 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB3
Chain IDs:C
Chain Length:275
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:I3LCH3 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit E
Chain IDs:D (auth: E)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:I3LSI7 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Chain IDs:E (auth: F)
Chain Length:127
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A4X1VEK9 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit
Chain IDs:F (auth: G)
Chain Length:172
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A4X1VKG7 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:G (auth: H)
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:I3LCB2 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB9
Chain IDs:H (auth: I)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:P60899 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Chain IDs:I (auth: J)
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A8W4F9W9
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB11-a
Chain IDs:J (auth: K)
Chain Length:117
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:F1RKE4 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase II, I and III subunit K
Chain IDs:K (auth: L)
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A4X1TRS6 Pfam ID:PF03604
Ligand Molecules
ZN
Primary Citation
Mechanism of mammalian transcriptional repression by noncoding RNA.
Nat.Struct.Mol.Biol. 32 607 612 (2025)
PMID: 39762629 DOI: 10.1038/s41594-024-01448-7

Abstact

Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.

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Primary Citation of related structures
8QEP