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- EMDB-63478: Human RNA Polymerase III de novo transcribing complex 5 on 7SK pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-63478
TitleHuman RNA Polymerase III de novo transcribing complex 5 on 7SK promoter (7SK-TC5)
Map dataPol III 7SK-TC5 main map
Sample
  • Complex: Human RNA Polymerase III de novo transcribing complex 5 on 7SK promoter (7SK-TC5)
Keywordsinitiation transcribing complex / TRANSCRIPTION/DNA/RNA / TRANSCRIPTION-DNA-RNA complex / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang Q / Ren Y / Jin Q / Chen X / Xu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2025
Title: Structural insights into human Pol III transcription initiation in action.
Authors: Qianmin Wang / Yulei Ren / Qianwei Jin / Xizi Chen / Yanhui Xu /
Abstract: RNA polymerase III (Pol III) transcribes highly demanded RNAs grouped into three types of classical promoters, including type 1 (5S rRNA), type 2 (tRNA) and type 3 (short non-coding RNAs, such as U6, ...RNA polymerase III (Pol III) transcribes highly demanded RNAs grouped into three types of classical promoters, including type 1 (5S rRNA), type 2 (tRNA) and type 3 (short non-coding RNAs, such as U6, 7SK and RNase H1) promoters. While structures of the Pol III preinitiation complex (PIC) and elongation complex (EC) have been determined, the mechanism underlying the transition from initiation to elongation remains unclear. Here we reconstituted seven human Pol III transcribing complexes (TC4, TC5, TC6, TC8, TC10, TC12 and TC13) halted on U6 promoters with nascent RNAs of 4-13 nucleotides. Cryo-electron microscopy structures captured initially transcribing complexes (ITCs; TC4 and TC5) and ECs (TC6-13). Together with KMnO footprinting, the data reveal extensive modular rearrangements: the transcription bubble expands from PIC to TC5, followed by general transcription factor (GTF) dissociation and abrupt bubble collapse from TC5 to TC6, marking the ITC-EC transition. In TC5, SNAPc and TFIIIB remain bound to the promoter and Pol III, while the RNA-DNA hybrid adopts a tilted conformation with template DNA blocked by BRF2, a TFIIIB subunit. Hybrid forward translocation during ITC-EC transition triggers BRF2-finger retraction, GTF release and transcription-bubble collapse. Pol III then escapes the promoter while GTFs stay bound upstream, potentially enabling reinitiation. These findings reveal molecular insights into Pol III dynamics and reinitiation mechanisms on type 3 promoters of highly demanded small RNAs, with the earliest documented initiation-elongation transition for an RNA polymerase.
History
DepositionFeb 18, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63478.png

Downloads & links

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Map

FileDownload / File: emd_63478.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPol III 7SK-TC5 main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 320 pix.
= 426.88 Å		1.33 Å/pix.
x 320 pix.
= 426.88 Å		1.33 Å/pix.
x 320 pix.
= 426.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.334 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-2.555947 - 5.1928124
Average (Standard dev.)0.005729153 (±0.09044588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 426.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Pol III 7SK-TC5 half map 1

Fileemd_63478_half_map_1.map
AnnotationPol III 7SK-TC5 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pol III 7SK-TC5 half map 2

Fileemd_63478_half_map_2.map
AnnotationPol III 7SK-TC5 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human RNA Polymerase III de novo transcribing complex 5 on 7SK pr...

EntireName: Human RNA Polymerase III de novo transcribing complex 5 on 7SK promoter (7SK-TC5)
Components
  • Complex: Human RNA Polymerase III de novo transcribing complex 5 on 7SK promoter (7SK-TC5)

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Supramolecule #1: Human RNA Polymerase III de novo transcribing complex 5 on 7SK pr...

SupramoleculeName: Human RNA Polymerase III de novo transcribing complex 5 on 7SK promoter (7SK-TC5)
type: complex / ID: 1 / Parent: 0
Details: RNA polymerase III transcribing complex 5 RNA polymerase III in initiation transcription stage
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

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
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: EMDB MAP
EMDB ID:

35722

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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