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- EMDB-57394: Focused refinement map of nucleosome of RNA polymerase II initial... -

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Basic information

Entry
Database: EMDB / ID: EMD-57394
TitleFocused refinement map of nucleosome of RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome
Map datafocused refinement map
Sample
  • Complex: RNA polymerase II elongation complex with the +1 nucleosome
KeywordsRNA polymerase II / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsZhan Y / Abril-Garrido J / Dienemann C / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published / Year: 2026
Title: RNA polymerase II elongation complex with the +1 nucleosome
Authors: Zhan Y / Abril-Garrido J
History
DepositionApr 9, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57394.png

Downloads & links

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Map

FileReleased
Annotationfocused refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 252. Å		1.05 Å/pix.
x 240 pix.
= 252. Å		1.05 Å/pix.
x 240 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0197
Minimum - Maximum-0.020454386 - 0.0745382
Average (Standard dev.)0.00031638343 (±0.0029804849)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_57394_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_57394_half_map_2.map
Annotationhalf 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 : RNA polymerase II elongation complex with the +1 nucleosome

EntireName: RNA polymerase II elongation complex with the +1 nucleosome
Components
  • Complex: RNA polymerase II elongation complex with the +1 nucleosome

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Supramolecule #1: RNA polymerase II elongation complex with the +1 nucleosome

SupramoleculeName: RNA polymerase II elongation complex with the +1 nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#38
Source (natural)Organism: Homo sapiens (human)

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
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: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 50163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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