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- EMDB-51278: Cryo-EM structure of Vibrio cholerae RNA polymerase dimer with To... -

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Basic information

Entry
Database: EMDB / ID: EMD-51278
TitleCryo-EM structure of Vibrio cholerae RNA polymerase dimer with ToxR and TcpP transcription factors and a toxT promoter DNA fragment
Map dataTAC toxT L RNAP dimer raw map
Sample
  • Complex: Virulent transcription complex #6
KeywordsRNA polymerase / Open promoter complex / toxT / Vibrio cholerae / ToxR / TcpP TRANSCRIPTION / TRANSCRIPTION
Biological speciesVibrio cholerae O395 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsAlcaide-Jimenez A / Baudin F / Canals A / Machon C / Murciano B / Fabrega-Ferrer M / Bantysh O / Perez-Luque R / Krukonis ES / Muller CW / Coll M
Funding support Spain, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-12141GB-100 Spain
Generalitat de Catalunya2021SGR00423 Spain
CitationJournal: Science Advances / Year: 2025
Title: Structures of Vibrio cholerae transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes
Authors: Alcaide-Jimenez A / Canals A / Baudin F / Machon C / Fabrega-Ferrer M / Bantysh O / Perez-Luque R / Murciano B / Mohammad AA / Rowse MJ / Ferracciolo JM / Krukonis ES / Muller CW / Coll M
History
DepositionAug 6, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51278.png

Downloads & links

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Map

FileDownload / File: emd_51278.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTAC toxT L RNAP dimer raw map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.19 Å/pix.
x 512 pix.
= 1122.816 Å		2.19 Å/pix.
x 512 pix.
= 1122.816 Å		2.19 Å/pix.
x 512 pix.
= 1122.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.193 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.274
Minimum - Maximum-0.47620893 - 2.071481
Average (Standard dev.)-0.0022916116 (±0.038380392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1122.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: TAC toxT L RNAP dimer sharpened map

Fileemd_51278_additional_1.map
AnnotationTAC toxT L RNAP dimer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TAC toxT L RNAP dimer half map B

Fileemd_51278_half_map_1.map
AnnotationTAC toxT L RNAP dimer half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TAC toxT L RNAP dimer half map A

Fileemd_51278_half_map_2.map
AnnotationTAC toxT L RNAP dimer half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Virulent transcription complex #6

EntireName: Virulent transcription complex #6
Components
  • Complex: Virulent transcription complex #6

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Supramolecule #1: Virulent transcription complex #6

SupramoleculeName: Virulent transcription complex #6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Vibrio cholerae O395 (bacteria)

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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

Concentration0.4 mg/mL
BufferpH: 8
Details: 10 mM HEPES pH 8.0, 500 mM NaCl, 1 mM DTT and 0.1 mM EDTA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.71 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Local resolution with C2 symmetry expansion / Number images used: 46334
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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