9EI2 | pdb_00009ei2

Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to an apo RECQL5 helicase (RECQL5 IRI Module focused-classified)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into transcriptional regulation by the helicase RECQL5.

Florez Ariza, A.J.Lue, N.Z.Grob, P.Kaeser, B.Fang, J.Kassube, S.A.Nogales, E.

(2025) Nat Struct Mol Biol 32: 1721-1730

  • DOI: https://doi.org/10.1038/s41594-025-01611-8
  • Primary Citation of Related Structures:  
    9EHZ, 9EI1, 9EI2, 9EI3, 9EI4

  • PubMed Abstract: 

    Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human 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, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.


  • Organizational Affiliation
    • California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,970Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (UniProt), 2.7.7.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
PHAROS:  P24928
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24928
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase Q5B [auth U]991Homo sapiensMutation(s): 0 
Gene Names: RECQL5RECQ5
EC: 5.6.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for O94762 (Homo sapiens)
Explore O94762 
Go to UniProtKB:  O94762
PHAROS:  O94762
GTEx:  ENSG00000108469 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94762
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesR35 GM127018

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-24
    Changes: Data collection, Database references