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- EMDB-51258: RNAP-TopoI complex on duplex scaffold - focused map (RNAP beta pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-51258
TitleRNAP-TopoI complex on duplex scaffold - focused map (RNAP beta protrusion and lobe)
Map dataRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - deepemhanced map
Sample
  • Complex: RNAP-TopoI complex on duplex scaffold
    • Complex: DNA-directed RNA polymerase elongation complex
    • Complex: DNA topoisomerase 1
KeywordsRNA polymerase / topoisomerase / DNA topology / TRANSCRIPTION
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsVidmar V / Weixlbaumer A / Lamour V
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0040-01 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05 France
CitationJournal: To Be Published
Title: DNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli
Authors: Vidmar V / Borde C / Bruno L / Takacs M / Batisse C / Saint-Andre C / Zhu C / Espeli O / Lamour V / Weixlbaumer A
History
DepositionAug 5, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51258.png

Downloads & links

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Map

FileDownload / File: emd_51258.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - deepemhanced map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242
Minimum - Maximum-0.04881287 - 1.4829023
Average (Standard dev.)0.0017011849 (±0.021908069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51258_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_51258_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: RNAP-TopoI complex on duplex scaffold focused refinement (RNAP...

Fileemd_51258_additional_1.map
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RNAP-TopoI complex on duplex scaffold focused refinement (RNAP...

Fileemd_51258_half_map_1.map
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RNAP-TopoI complex on duplex scaffold focused refinement (RNAP...

Fileemd_51258_half_map_2.map
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNAP-TopoI complex on duplex scaffold

EntireName: RNAP-TopoI complex on duplex scaffold
Components
  • Complex: RNAP-TopoI complex on duplex scaffold
    • Complex: DNA-directed RNA polymerase elongation complex
    • Complex: DNA topoisomerase 1

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Supramolecule #1: RNAP-TopoI complex on duplex scaffold

SupramoleculeName: RNAP-TopoI complex on duplex scaffold / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightTheoretical: 100 KDa

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Supramolecule #2: DNA-directed RNA polymerase elongation complex

SupramoleculeName: DNA-directed RNA polymerase elongation complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#9
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: DNA topoisomerase 1

SupramoleculeName: DNA topoisomerase 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES/KOH
150.0 mMpotassium acetate
5.0 mMmagnesium acetate
0.01 mMzinc chloride
2.0 mMDTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.6 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: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113760
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6alh

source_name: PDB, initial_model_type: experimental model

4rul

source_name: PDB, initial_model_type: experimental model
DetailsInitial rigid body fit was done in UCSF Chimera, followed by flexible fitting in Isolde. The entire model was further refined in Phenix and Coot.
RefinementSpace: REAL

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