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- EMDB-52442: Focused refined map of PAF complex in the EC-DSIF-PAF-SPT6-RECQL5... -

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Basic information

Entry
Database: EMDB / ID: EMD-52442
TitleFocused refined map of PAF complex in the EC-DSIF-PAF-SPT6-RECQL5 complex
Map dataSharpened focused refined map of PAF
Sample
  • Complex: Pol II-DSIF-PAF-SPT6-RECQL5 complex
Keywordstranscription elongation / DNA helicase / transcription-coupled repair / RNA polymerase II / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsZhang L / Zhang S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/30 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
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
DepositionDec 31, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52442.png

Downloads & links

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Map

FileDownload / File: emd_52442.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened focused refined map of PAF
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 293.616 Å		0.82 Å/pix.
x 360 pix.
= 293.616 Å		0.82 Å/pix.
x 360 pix.
= 293.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1331776 - 1.8258247
Average (Standard dev.)0.00038689002 (±0.03130371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 293.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52442_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened focused refined map of PAF

Fileemd_52442_additional_1.map
AnnotationNon-sharpened focused refined map of PAF
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for the focused refined map of PAF

Fileemd_52442_half_map_1.map
AnnotationHalf map for the focused refined map of PAF
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for the focused refined map of PAF

Fileemd_52442_half_map_2.map
AnnotationHalf map for the focused refined map of PAF
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pol II-DSIF-PAF-SPT6-RECQL5 complex

EntireName: Pol II-DSIF-PAF-SPT6-RECQL5 complex
Components
  • Complex: Pol II-DSIF-PAF-SPT6-RECQL5 complex

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Supramolecule #1: Pol II-DSIF-PAF-SPT6-RECQL5 complex

SupramoleculeName: Pol II-DSIF-PAF-SPT6-RECQL5 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT
GridModel: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.25
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 71964 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7b0y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 314016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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