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- EMDB-57403: focused refinement map of core PIC in RNA polymerase II pre-initi... -

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Basic information

Entry
Database: EMDB / ID: EMD-57403
Titlefocused refinement map of core PIC in RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome
Map datamap filtered based on local resolution and sharpened
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: 3.6 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 10, 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_57403.png

Downloads & links

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Map

FileReleased
Annotationmap filtered based on local resolution and sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 504. Å		1.05 Å/pix.
x 480 pix.
= 504. Å		1.05 Å/pix.
x 480 pix.
= 504. 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: 6.52
Minimum - Maximum-38.332459999999998 - 61.163179999999997
Average (Standard dev.)0.00041895758 (±0.93672836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: half map

Fileemd_57403_additional_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_57403_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_57403_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-#36
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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 19577
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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