9EI1 image
Entry Detail
PDB ID:
9EI1
EMDB ID:
Title:
Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-11-25
Release Date:
2025-03-05
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB1
Chain IDs:A
Chain Length:1970
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB2
Chain IDs:B
Chain Length:1174
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB3
Chain IDs:C
Chain Length:275
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB4
Chain IDs:D
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Chain IDs:E
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Chain IDs:F
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB7
Chain IDs:G
Chain Length:172
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:H
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB9
Chain IDs:I
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Chain IDs:J
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB11-a
Chain IDs:K
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Chain IDs:L
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:Non-template DNA, nucleic acid scaffold
Chain IDs:M (auth: N)
Chain Length:43
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:RNA, nucleic acid scaffold
Chain IDs:N (auth: P)
Chain Length:20
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:Template DNA, nucleic acid scaffold
Chain IDs:O (auth: T)
Chain Length:28
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:ATP-dependent DNA helicase Q5
Mutations:D157A
Chain IDs:P (auth: U)
Chain Length:991
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structural insights into transcriptional regulation by the helicase RECQL5.
Biorxiv ? ? ? (2025)
PMID: 39975028 DOI: 10.1101/2025.01.29.634372

Abstact

Transcription and its regulation pose a major challenge for genome stability. The helicase RECQL5 has been proposed as an important factor to help safeguard the genome, and is the only member of the human RecQ helicase family that directly binds to RNA Polymerase II (Pol II) and affects its progression. RECQL5 mitigates transcription stress and genome instability in cells, yet the molecular mechanism underlying this phenomenon is unclear. Here, we employ cryo-electron microscopy (cryo-EM) to determine the structures of stalled Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that RECQL5 can modulate the Pol II translocation state. In its nucleotide-free state, RECQL5 mechanically twists the downstream DNA in the EC, and upon nucleotide binding, it undergoes a conformational change that allosterically induces Pol II towards a post-translocation state. We propose this mechanism may help restart Pol II elongation and therefore contribute to reduction of transcription stress.

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