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- EMDB-72554: Escherichia coli transcription-translation loosely coupled comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-72554
TitleEscherichia coli transcription-translation loosely coupled complex complex (TTC-LC^walked) containing mRNA with a 39 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site - Map 1
Map data
Sample
  • Complex: Transcription-Translation coupled complex
    • Organelle or cellular component: ribosome
KeywordsTranscription-translation coupled complex / TRANSCRIPTION
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShandilya S / Molodtsov 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)GM041376 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of long-range transcription-translation coupling.
Authors: Chengyuan Wang / Vadim Molodtsov / Shashank Shandilya / Linlin You / Jing Zhang / Konstantin Kuznedelov / Bryce E Nickels / Jason T Kaelber / Gregor Blaha / Richard H Ebright /
Abstract: Structures recently have been reported of molecular assemblies that mediate transcription-translation coupling in . In these molecular assemblies, termed "coupled transcription-translation complexes" ...Structures recently have been reported of molecular assemblies that mediate transcription-translation coupling in . In these molecular assemblies, termed "coupled transcription-translation complexes" or "TTC-B," RNA polymerase (RNAP) directly interacts with the ribosome, the transcription elongation factor NusG or its paralog RfaH forms a bridge between RNAP and ribosome, and the transcription elongation factor NusA optionally forms a second bridge between RNAP and ribosome. Here, we report structures of coupled transcription-translation complexes having mRNA spacers between RNAP and ribosome longer than the maximum-length mRNA spacer compatible with formation of TTC-B. The results define a class of coupled transcription-translation complex, termed "TTC-LC," where "LC" denotes "long-range coupling." TTC-LC differs from TTC-B by a ~60° rotation and ~70 Å translation of RNAP relative to ribosome, resulting in loss of direct interactions between RNAP and ribosome and creation of a ~70 Å gap between RNAP and ribosome. TTC-LC accommodates long mRNA spacers by looping out mRNA from the gap between RNAP and ribosome. We present evidence that TTC-LC is a functional intermediate in assembling and disassembling TTC-B, mediating pre-TTC-B transcription-translation coupling before a ribosome catches up to RNAP, and mediating post-TTC-B transcription-translation coupling after a ribosome stops moving and RNAP continues moving. We show that TTC-B, but not TTC-LC, is severely defective in RNA-hairpin-dependent transcription termination, and that both TTC-B and TTC-LC are severely defective in Rho-dependent transcription termination.
History
DepositionSep 8, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72554.png

Downloads & links

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Map

FileDownload / File: emd_72554.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 512 pix.
= 666.624 Å		1.3 Å/pix.
x 512 pix.
= 666.624 Å		1.3 Å/pix.
x 512 pix.
= 666.624 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.22247523 - 1.0748618
Average (Standard dev.)-0.0023074327 (±0.048513476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 666.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72554_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_72554_half_map_2.map
Projections & Slices
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Sample components

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Entire : Transcription-Translation coupled complex

EntireName: Transcription-Translation coupled complex
Components
  • Complex: Transcription-Translation coupled complex
    • Organelle or cellular component: ribosome

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Supramolecule #1: Transcription-Translation coupled complex

SupramoleculeName: Transcription-Translation coupled complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#67
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: ribosome

SupramoleculeName: ribosome / type: organelle_or_cellular_component / ID: 2 / Parent: 1
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: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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