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Open data
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Basic information
| Entry | Database: PDB / ID: 9hwg | ||||||
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| Title | Structure of the transcribing Pol II-TCR-RECQL5 complex | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription elongation / DNA helicase / transcription-coupled repair / RNA polymerase II | ||||||
| Function / homology | Function and homology informationmitotic DNA-templated DNA replication / RNA polymerase inhibitor activity / negative regulation of double-strand break repair via nonhomologous end joining / chromosome separation / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / response to auditory stimulus / four-way junction helicase activity / DNA protection / transcription elongation factor complex ...mitotic DNA-templated DNA replication / RNA polymerase inhibitor activity / negative regulation of double-strand break repair via nonhomologous end joining / chromosome separation / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / response to auditory stimulus / four-way junction helicase activity / DNA protection / transcription elongation factor complex / regulation of transcription elongation by RNA polymerase II / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / mRNA Splicing - Major Pathway / mRNA Polyadenylation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair via classical nonhomologous end joining / single strand break repair / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / chromatin-protein adaptor activity / ATP-dependent chromatin remodeler activity / epigenetic programming in the zygotic pronuclei / transcription preinitiation complex / UV-damage excision repair / DNA metabolic process / ATP-dependent DNA damage sensor activity / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / negative regulation of transcription elongation by RNA polymerase II / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / Cul4B-RING E3 ubiquitin ligase complex / RNA polymerase II complex binding / RNA Polymerase I Transcription Initiation / ubiquitin ligase complex scaffold activity / response to UV / negative regulation of adipose tissue development / DNA 3'-5' helicase / regulation of cellular response to stress / viral release from host cell / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / 3'-5' DNA helicase activity / cullin family protein binding / protein tyrosine kinase activator activity / ATP-dependent activity, acting on DNA / translation elongation factor activity / neurogenesis / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / protein autoubiquitination / termination of RNA polymerase III transcription / positive regulation of double-strand break repair via homologous recombination / transcription initiation at RNA polymerase III promoter / ubiquitin-like ligase-substrate adaptor activity / DNA damage checkpoint signaling / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / protein localization to chromatin / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / replication fork Similarity search - Function | ||||||
| Biological species | Homo sapiens (human)![]() synthetic construct (others) | ||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zhang, L. / Zhang, S. | ||||||
| Funding support | United Kingdom, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation. Authors: Luojia Zhang / Yuliya Gordiyenko / Tomos Morgan / Catarina Franco / Ana Tufegdžić Vidaković / Suyang Zhang / ![]() Abstract: Abnormally fast transcription elongation can lead to detrimental consequences such as transcription-replication collisions, altered alternative splicing patterns and genome instability. Therefore, ...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. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9hwg.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9hwg.ent.gz | 936.2 KB | Display | PDB format |
| PDBx/mmJSON format | 9hwg.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/9hwg ftp://data.pdbj.org/pub/pdb/validation_reports/hw/9hwg | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 52449MC ![]() 9hvoC ![]() 9hvqC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEGIK
| #1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A8D1DPV6, DNA-directed RNA polymerase |
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| #2: Protein | Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase |
| #3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA polymerase ... , 2 types, 2 molecules DL
| #4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ
| #6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA chain , 2 types, 2 molecules NT
| #13: DNA chain | Mass: 14494.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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| #16: DNA chain | Mass: 14269.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 4 types, 4 molecules Ocde
| #14: Protein | Mass: 109024.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94762, DNA 3'-5' helicase |
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| #19: Protein | Mass: 80721.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UVSSA, KIAA1530 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2YD98 |
| #20: Protein | Mass: 127097.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531 |
| #21: Protein | Mass: 9475.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOF1, hCG_29982 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A024R7E8 |
-RNA chain , 1 types, 1 molecules P
| #15: RNA chain | Mass: 14490.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-DNA excision repair protein ERCC- ... , 2 types, 2 molecules ab
| #17: Protein | Mass: 44107.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC8, CKN1, CSA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13216 |
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| #18: Protein | Mass: 168673.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC6, CSB / Production host: Trichoplusia ni (cabbage looper)References: UniProt: Q03468, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
-Non-polymers , 2 types, 12 molecules 


| #22: Chemical | ChemComp-ZN / #23: Chemical | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: PolII-TCR-RECQL5 complex / Type: COMPLEX / Entity ID: #1-#21 / Source: RECOMBINANT |
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| Source (natural) | Organism: Homo sapiens (human) |
| Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
| Buffer solution | pH: 7.5 Details: 20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 |
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Electron dose: 36.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 |
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Processing
| EM software | Name: PHENIX / Version: 1.21.2_5419: / Category: model refinement |
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
| 3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19458 / Num. of class averages: 1 / Symmetry type: POINT |
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About Yorodumi




Homo sapiens (human)

United Kingdom, 1items
Citation






PDBj




































































Trichoplusia ni (cabbage looper)
FIELD EMISSION GUN