9EHZ | pdb_00009ehz

Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4A [auth D]142Homo sapiensMutation(s): 0 
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PHAROS:  O15514
GTEx:  ENSG00000144231 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1B [auth E]210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099817 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2C [auth F]127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100142 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7D [auth G]172Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168002 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3E [auth H]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163882 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9F [auth I]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105258 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5G [auth J]67Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177700 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aH [auth K]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000005075 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4I [auth L]58Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147669 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1M [auth A]1,970Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (UniProt), 2.7.7.48 (UniProt)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2N [auth B]1,174Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (UniProt), 2.7.7.48 (UniProt)
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GTEx:  ENSG00000047315 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3O [auth C]275Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102978 
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Entity ID: 10
MoleculeChains LengthOrganismImage
Non-template DNA, nucleic acid scaffoldJ [auth N]43Homo sapiens
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Entity ID: 11
MoleculeChains LengthOrganismImage
RNA, nucleic acid scaffoldK [auth P]20Homo sapiens
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Entity ID: 12
MoleculeChains LengthOrganismImage
Template DNA, nucleic acid scaffoldL [auth T]28Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
P [auth I]
Q [auth I]
R [auth J]
S [auth L]
U [auth A]
P [auth I],
Q [auth I],
R [auth J],
S [auth L],
U [auth A],
V [auth A],
W [auth B],
X [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
T [auth P]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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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