9HVQ | pdb_00009hvq

Structure of the transcribing Pol II-DSIF-PAF-SPT6-RECQL5 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation.

Zhang, L.Gordiyenko, Y.Morgan, T.Franco, C.Tufegdzic Vidakovic, A.Zhang, S.

(2025) Nat Struct Mol Biol 32: 1731-1740

  • DOI: https://doi.org/10.1038/s41594-025-01586-6
  • Primary Citation of Related Structures:  
    9HVO, 9HVQ, 9HWG

  • PubMed Abstract: 

    Abnormally fast transcription elongation can lead to detrimental consequences such as transcription-replication collisions, altered alternative splicing patterns and genome instability. Therefore, elongating RNA polymerase II (Pol II) requires mechanisms to slow its progression, yet the molecular basis of transcription braking remains unclear. RECQL5 is a DNA helicase that functions as a general elongation factor by slowing down Pol II. Here we report cryo-electron microscopy structures of human RECQL5 bound to multiple transcription elongation complexes. Combined with biochemical analysis, we identify an α-helix of RECQL5 responsible for binding Pol II and slowdown of transcription elongation. We further reveal that the transcription-coupled DNA repair (TCR) complex allows Pol II to overcome RECQL5-induced transcription braking through concerted actions of its translocase activity and competition with RECQL5 for engaging Pol II. Additionally, RECQL5 inhibits TCR-mediated Pol II ubiquitination to prevent activation of the DNA repair pathway. Our results suggest a model in which RECQL5 and the TCR complex coordinately regulate transcription elongation rates to ensure transcription efficiency while maintaining genome stability.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,970Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa)
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UniProt GroupA0A8D1DPV6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofa domesticusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D142Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit172Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofa domesticusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A4X1VYD0 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a117Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II, I and III subunit K58Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT61,726Homo sapiensMutation(s): 0 
Gene Names: SUPT6HKIAA0162SPT6H
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PHAROS:  Q7KZ85
GTEx:  ENSG00000109111 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase Q5991Homo sapiensMutation(s): 0 
Gene Names: RECQL5RECQ5
EC: 5.6.2.4
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GTEx:  ENSG00000108469 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9 homolog1,173Homo sapiensMutation(s): 0 
Gene Names: CTR9KIAA0155SH2BP1
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GTEx:  ENSG00000198730 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein LEO1S [auth U]666Homo sapiensMutation(s): 0 
Gene Names: LEO1RDL
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GTEx:  ENSG00000166477 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated factor 1 homologT [auth V]531Homo sapiensMutation(s): 0 
Gene Names: PAF1PD2
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GTEx:  ENSG00000006712 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 61U [auth W]305Homo sapiensMutation(s): 0 
Gene Names: WDR61
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GTEx:  ENSG00000140395 
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UniProt GroupQ9GZS3
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ParafibrominV [auth X]531Homo sapiensMutation(s): 0 
Gene Names: CDC73C1orf28HRPT2
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PHAROS:  Q6P1J9
GTEx:  ENSG00000134371 
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UniProt GroupQ6P1J9
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4W [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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PHAROS:  P63272
GTEx:  ENSG00000213246 
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UniProt GroupP63272
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5X [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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PHAROS:  O00267
GTEx:  ENSG00000196235 
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA63synthetic construct
Sequence Annotations
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Entity ID: 16
MoleculeChains LengthOrganismImage
RNA15synthetic construct
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Entity ID: 18
MoleculeChains LengthOrganismImage
Template DNAR [auth T]48synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth C]
DA [auth I]
EA [auth I]
FA [auth J]
BA [auth B],
CA [auth C],
DA [auth I],
EA [auth I],
FA [auth J],
GA [auth L],
Y [auth A],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/30

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Data collection, Database references