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- EMDB-27918: Escherichia coli Rho-dependent transcription pre-termination comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-27918
TitleEscherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Map dataEscherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Sample
  • Complex: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsMolodtsov V / Wang C / Ebright RH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Nature / Year: 2023
Title: Structural basis of Rho-dependent transcription termination.
Authors: Vadim Molodtsov / Chengyuan Wang / Emre Firlar / Jason T Kaelber / Richard H Ebright /
Abstract: Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription- ...Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription-translation-coupling quality control in Escherichia coli. Here we report the preparation of complexes that are functional in factor-dependent transcription termination from Rho, NusG, RNA polymerase (RNAP), and synthetic nucleic acid scaffolds, and we report cryogenic electron microscopy structures of the complexes. The structures show that functional factor-dependent pre-termination complexes contain a closed-ring Rho hexamer; have RNA threaded through the central channel of Rho; have 60 nucleotides of RNA interacting sequence-specifically with the exterior of Rho and 6 nucleotides of RNA interacting sequence-specifically with the central channel of Rho; have Rho oriented relative to RNAP such that ATP-dependent translocation by Rho exerts mechanical force on RNAP; and have NusG bridging Rho and RNAP. The results explain five decades of research on Rho and provide a foundation for understanding Rho's function.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of Rho-dependent transcription termination
Authors: Molodtsov V / Wang C / Firlar E / Kaelber JT / Ebright RH
History
DepositionAug 22, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27918.png

Downloads & links

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Map

FileDownload / File: emd_27918.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEscherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.0038570082 - 0.019934803
Average (Standard dev.)-7.8327765e-05 (±0.0012424763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1 Escherichia coli Rho-dependent transcription pre-termination complex...

Fileemd_27918_half_map_1.map
AnnotationHalf-map 1 Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half-map 2 Escherichia coli Rho-dependent transcription pre-termination complex...

Fileemd_27918_half_map_2.map
AnnotationHalf-map 2 Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia coli Rho-dependent transcription pre-termination comp...

EntireName: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
Components
  • Complex: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG

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Supramolecule #1: Escherichia coli Rho-dependent transcription pre-termination comp...

SupramoleculeName: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG
type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270373
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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