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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 | ||||||
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![]() | TRANSCRIPTION / transcription elongation / DNA helicase / transcription-coupled repair / RNA polymerase II | ||||||
Function / homology | ![]() RNA polymerase inhibitor activity / mitotic DNA-templated DNA replication / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / chromosome separation / cellular response to camptothecin / regulation of transcription elongation by RNA polymerase II / replication-born double-strand break repair via sister chromatid exchange / B-WICH complex ...RNA polymerase inhibitor activity / mitotic DNA-templated DNA replication / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / chromosome separation / cellular response to camptothecin / regulation of transcription elongation by RNA polymerase II / replication-born double-strand break repair via sister chromatid exchange / B-WICH complex / DNA protection / single strand break repair / positive regulation by virus of viral protein levels in host cell / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / chromatin-protein adaptor activity / response to superoxide / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / photoreceptor cell maintenance / epigenetic programming in the zygotic pronuclei / ATP-dependent chromatin remodeler activity / Cul4-RING E3 ubiquitin ligase complex / nuclear lumen / UV-damage excision repair / response to UV-B / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / biological process involved in interaction with symbiont / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / ATP-dependent DNA damage sensor activity / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of transcription by RNA polymerase I / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / cullin family protein binding / viral release from host cell / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / protein tyrosine kinase activator activity / site of DNA damage / RNA Polymerase I Transcription Initiation / pyrimidine dimer repair / response to X-ray / ATP-dependent activity, acting on DNA / ectopic germ cell programmed cell death / positive regulation of transcription initiation by RNA polymerase II / translation elongation factor activity / transcription by RNA polymerase III / negative regulation of double-strand break repair via homologous recombination / positive regulation of viral genome replication / transcription by RNA polymerase I / positive regulation of double-strand break repair via homologous recombination / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / response to UV / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / protein autoubiquitination / JNK cascade / neurogenesis / DNA helicase activity / positive regulation of gluconeogenesis / DNA-directed RNA polymerase complex / isomerase activity / positive regulation of DNA repair / DNA damage checkpoint signaling / transcription elongation factor complex / regulation of DNA-templated transcription elongation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Zhang, L. / Zhang, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 936.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 170.3 KB | Display | |
Data in CIF | ![]() | 269 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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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.) ![]() ![]() |
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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.) ![]() ![]() |
#20: Protein | Mass: 127097.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#21: Protein | Mass: 9475.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-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.) ![]() ![]() |
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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.) ![]() ![]() 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: ![]() |
Source (recombinant) | Organism: ![]() |
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: ![]() |
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 |