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- EMDB-57789: Focused map of the +1 nucleosome (ITC6) -

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Basic information

Entry
Database: EMDB / ID: EMD-57789
TitleFocused map of the +1 nucleosome (ITC6)
Map dataRefinement map
Sample
  • Complex: Initially transcribing complex of a 6 nt RNA in the presence of a +1 nucleosome
    • Complex: General transcription factor IIH
    • Complex: Mammalian RNA polymerase II
    • Complex: Nucleosome (protein)
    • Complex: Nucleosome (DNA)
    • Complex: General transcription factor IIB
    • Complex: Transcription initiation factor IID
    • Complex: General transcription factor IIF
    • Complex: General transcription factor IIA
    • Complex: General transcription factor IIE
KeywordsMammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Xenopus laevis (African clawed frog) / unidentified adenovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZhan Y / Abril-Garrido J / Grabbe F / Seweryn P / Neef U / Dienemann C / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2026
Title: The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation.
Authors: Yumeng Zhan / Julio Abril-Garrido / Frauke Grabbe / Paulina Seweryn / Ute Neef / Christian Dienemann / Patrick Cramer /
Abstract: Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre- ...Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre-initiation complex (PIC) assembly and RNA Pol II pausing, but its function in transcription initiation and the transition to elongation remains unclear. Here, we investigate the transcription initiation-elongation transition in vitro using DNA templates containing a +1 nucleosome and present cryo-electron microscopy (cryo-EM) structures of five intermediate states. First, after PIC assembly, ATP binding to TFIIH enables the +1 nucleosome to evict TFIID from the PIC. Following DNA opening, the +1 nucleosome stimulates TFIIH translocase activity and initial RNA synthesis. Finally, after DNA bubble rewinding, the +1 nucleosome removes TFIIH from the early elongation complex for promoter escape. Our findings show that the +1 nucleosome not only acts passively in PIC assembly and RNA Pol II pausing but rather has active functions during the initiation-elongation transition of transcription.
History
DepositionApr 27, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57789.png

Downloads & links

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Map

FileDownload / File: emd_57789.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefinement 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: 0.019
Minimum - Maximum-0.014211527 - 0.08548818
Average (Standard dev.)0.00038445668 (±0.004106366)
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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Mask #1

Fileemd_57789_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map

Fileemd_57789_additional_1.map
AnnotationPostprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution map

Fileemd_57789_additional_2.map
AnnotationLocal resolution map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_57789_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_57789_half_map_2.map
AnnotationHalf map 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 : Initially transcribing complex of a 6 nt RNA in the presence of a...

EntireName: Initially transcribing complex of a 6 nt RNA in the presence of a +1 nucleosome
Components
  • Complex: Initially transcribing complex of a 6 nt RNA in the presence of a +1 nucleosome
    • Complex: General transcription factor IIH
    • Complex: Mammalian RNA polymerase II
    • Complex: Nucleosome (protein)
    • Complex: Nucleosome (DNA)
    • Complex: General transcription factor IIB
    • Complex: Transcription initiation factor IID
    • Complex: General transcription factor IIF
    • Complex: General transcription factor IIA
    • Complex: General transcription factor IIE

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Supramolecule #1: Initially transcribing complex of a 6 nt RNA in the presence of a...

SupramoleculeName: Initially transcribing complex of a 6 nt RNA in the presence of a +1 nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#59
Molecular weightTheoretical: 2.7 MDa

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Supramolecule #2: General transcription factor IIH

SupramoleculeName: General transcription factor IIH / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 490 KDa

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Supramolecule #3: Mammalian RNA polymerase II

SupramoleculeName: Mammalian RNA polymerase II / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#14, #34-#41
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 516 KDa

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Supramolecule #4: Nucleosome (protein)

SupramoleculeName: Nucleosome (protein) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #52-#59
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #5: Nucleosome (DNA)

SupramoleculeName: Nucleosome (DNA) / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #43, #47
Source (natural)Organism: unidentified adenovirus

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Supramolecule #6: General transcription factor IIB

SupramoleculeName: General transcription factor IIB / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #42
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Transcription initiation factor IID

SupramoleculeName: Transcription initiation factor IID / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #15-#33, #44
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: General transcription factor IIF

SupramoleculeName: General transcription factor IIF / type: complex / ID: 8 / Parent: 1 / Macromolecule list: #45-#46
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #9: General transcription factor IIA

SupramoleculeName: General transcription factor IIA / type: complex / ID: 9 / Parent: 1 / Macromolecule list: #48-#49
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #10: General transcription factor IIE

SupramoleculeName: General transcription factor IIE / type: complex / ID: 10 / Parent: 1 / Macromolecule list: #50-#51
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
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 88900 / Average exposure time: 3.0 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 12714020
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 37259
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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