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- EMDB-18888: Elongation complex of RNA polymerase II (EC of RNAPII) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-18888
TitleElongation complex of RNA polymerase II (EC of RNAPII)
Map data
Sample
  • Complex: RNAP II EC -- RECQ5(delta625-825)
KeywordsRNA polymerase II / transcription inhibition / electron cryomicroscopy / electron cryotomography / TRANSCRIPTION
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSkubnik K / Sebesta M / Stefl R
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation Czech Republic
CitationJournal: To Be Published
Title: Spatial organization of RNA polymerase II-RECQ5 transcriptional condensate
Authors: Sebesta M / Skubnik K / Stefl R
History
DepositionNov 14, 2023-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18888.png

Downloads & links

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Map

FileDownload / File: emd_18888.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 352 pix.
= 275.616 Å		0.78 Å/pix.
x 352 pix.
= 275.616 Å		0.78 Å/pix.
x 352 pix.
= 275.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.783 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0937
Minimum - Maximum-0.43799698 - 0.73456556
Average (Standard dev.)0.0008740622 (±0.025801934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 275.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18888_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18888_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18888_half_map_2.map
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 II EC -- RECQ5(delta625-825)

EntireName: RNAP II EC -- RECQ5(delta625-825)
Components
  • Complex: RNAP II EC -- RECQ5(delta625-825)

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Supramolecule #1: RNAP II EC -- RECQ5(delta625-825)

SupramoleculeName: RNAP II EC -- RECQ5(delta625-825) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 500 KDa

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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
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3227 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 334500
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56966
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab initio model was generated in CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Avg.num./class: 45000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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