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- EMDB-51958: Focused map #2 of the cryo-EM structure of Vibrio cholerae RNA po... -

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Basic information

Entry
Database: EMDB / ID: EMD-51958
TitleFocused map #2 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR and TcpP transcription factors and bound to a toxT promoter DNA fragment
Map dataTAC_toxT_L Map K Multibody refinement body 2. Unsharpened map.
Sample
  • Complex: Virulent transcription complex #5
    • Complex: DNA-directed RNA polymerase
    • Complex: Double stranded DNA
KeywordsRNA polymerase / Transcription Activation Complex / toxT / ToxR / TcpP / Vibrio cholerae / TRANSCRIPTION
Biological speciesVibrio cholerae O395 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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: Sci Adv / Year: 2026
Title: Structures of transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes.
Authors: Adrià Alcaide-Jiménez / Albert Canals / Florence Baudin / Cristina Machón / Montserrat Fàbrega-Ferrer / Olga Bantysh / Rosa Pérez-Luque / Brice Murciano / Ali A Mohammad / Michael J ...Authors: Adrià Alcaide-Jiménez / Albert Canals / Florence Baudin / Cristina Machón / Montserrat Fàbrega-Ferrer / Olga Bantysh / Rosa Pérez-Luque / Brice Murciano / Ali A Mohammad / Michael J Rowse / Joseph M Ferracciolo / Eric S Krukonis / Christoph W Müller / Miquel Coll /
Abstract: Activation of virulence in , the etiological agent of cholera disease, is mediated by two transmembrane one-component signal-transduction proteins, ToxR and TcpP, which are also transcription factors. ...Activation of virulence in , the etiological agent of cholera disease, is mediated by two transmembrane one-component signal-transduction proteins, ToxR and TcpP, which are also transcription factors. Using cryo-electron microscopy, we have solved five structures of the and transcription activation complexes, including the RNA polymerase (RNAP) holoenzyme, promoter DNAs, transcribed RNA, and their corresponding transcription factors, ToxR or TcpP and ToxR-TcpP, respectively. Activation is achieved through the interaction of ToxR or TcpP with the α-C-terminal repeat domain of RNAP where a single residue of the activator, a phenylalanine, appears to be the most critical contact, as confirmed by mutagenesis. No interactions of the transcription factors were observed with other subunits of the RNAP, i.e., the σ subunit as it occurs in the structurally related PhoB family of two-component transcription factors. The structures, and their comparison with our previously solved DNA promoter-ToxR x-ray structures, unveil the molecular mechanism of cholera virulence gene activation.
History
DepositionOct 30, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51958.png

Downloads & links

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Map

FileDownload / File: emd_51958.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTAC_toxT_L Map K Multibody refinement body 2. Unsharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.272 Å		0.73 Å/pix.
x 512 pix.
= 374.272 Å		0.73 Å/pix.
x 512 pix.
= 374.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00262
Minimum - Maximum-0.0062731323 - 0.012157821
Average (Standard dev.)-0.000046927777 (±0.0002842791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: TAC toxT L Map K Multibody refinement body 2. Sharpened map.

Fileemd_51958_additional_1.map
AnnotationTAC_toxT_L Map K Multibody refinement body 2. Sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TAC toxT L Map K unsharpened halfmap 1

Fileemd_51958_half_map_1.map
AnnotationTAC_toxT_L Map K unsharpened halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TAC toxT L Map K unsharpened halfmap 2.

Fileemd_51958_half_map_2.map
AnnotationTAC_toxT_L Map K unsharpened halfmap 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 : Virulent transcription complex #5

EntireName: Virulent transcription complex #5
Components
  • Complex: Virulent transcription complex #5
    • Complex: DNA-directed RNA polymerase
    • Complex: Double stranded DNA

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Supramolecule #1: Virulent transcription complex #5

SupramoleculeName: Virulent transcription complex #5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Supramolecule #2: DNA-directed RNA polymerase

SupramoleculeName: DNA-directed RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Vibrio cholerae O395 (bacteria)

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Supramolecule #3: Double stranded DNA

SupramoleculeName: Double stranded DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #4-#9
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, 150 mM NaCl, 1 mM DTT and 0.1 mM EDTA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 1.8 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88323
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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