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- EMDB-37412: De novo transcribing complex 9 (AdML9G), the initially transcribi... -

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Basic information

Entry
Database: EMDB / ID: EMD-37412
TitleDe novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS
Map data
Sample
  • Complex: De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS
    • Complex: TFIIDTranscription factor II D
    • Complex: RNA POLYMERASE II
    • Complex: TFIIATranscription factor II A
    • Complex: TFIIBTranscription factor II B
    • Complex: TFIIFTranscription factor II F
    • Complex: DNA
    • Complex: TFIIHTranscription factor II H
    • Complex: RNA
    • Complex: Alpha-amanitinΑ-Amanitin
    • Complex: TFIIETranscription factor II E
Keywordstranscribing complex / de novo transcription initiation / initially transcribing complex (ITC) / TRANSCRIPTION
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / synthetic construct (others) / Amanita phalloides (death cap)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.47 Å
AuthorsChen X / Liu W / Xu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2023
Title: Structural visualization of transcription initiation in action.
Authors: Xizi Chen / Weida Liu / Qianmin Wang / Xinxin Wang / Yulei Ren / Xuechun Qu / Wanjun Li / Yanhui Xu /
Abstract: Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted ...Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
History
DepositionSep 8, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37412.png

Downloads & links

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Map

FileDownload / File: emd_37412.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.334 Å
Density
Contour LevelBy AUTHOR: 0.633
Minimum - Maximum-0.5828849 - 2.3846607
Average (Standard dev.)0.04596556 (±0.18162386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 426.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Pol II module of AdML9G

Fileemd_37412_additional_1.map
AnnotationPol II module of AdML9G
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37412_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37412_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 : De novo transcribing complex 9 (AdML9G), the initially transcribi...

EntireName: De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS
Components
  • Complex: De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS
    • Complex: TFIIDTranscription factor II D
    • Complex: RNA POLYMERASE II
    • Complex: TFIIATranscription factor II A
    • Complex: TFIIBTranscription factor II B
    • Complex: TFIIFTranscription factor II F
    • Complex: DNA
    • Complex: TFIIHTranscription factor II H
    • Complex: RNA
    • Complex: Alpha-amanitinΑ-Amanitin
    • Complex: TFIIETranscription factor II E

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Supramolecule #1: De novo transcribing complex 9 (AdML9G), the initially transcribi...

SupramoleculeName: De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18

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Supramolecule #2: TFIID

SupramoleculeName: TFIID / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #11-#20, #31-#33
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA POLYMERASE II

SupramoleculeName: RNA POLYMERASE II / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #34-#45
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #4: TFIIA

SupramoleculeName: TFIIA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #21, #23
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: TFIIB

SupramoleculeName: TFIIB / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #24
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: TFIIF

SupramoleculeName: TFIIF / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #25-#26
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: DNA

SupramoleculeName: DNA / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #29-#30
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Supramolecule #8: TFIIH

SupramoleculeName: TFIIH / type: complex / ID: 8 / Parent: 1 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #9: RNA

SupramoleculeName: RNA / type: complex / ID: 9 / Parent: 1 / Macromolecule list: #10
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Supramolecule #10: Alpha-amanitin

SupramoleculeName: Alpha-amanitin / type: complex / ID: 10 / Parent: 1 / Macromolecule list: #9
Source (natural)Organism: Amanita phalloides (death cap)

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Supramolecule #11: TFIIE

SupramoleculeName: TFIIE / type: complex / ID: 11 / Parent: 1 / Macromolecule list: #27-#28
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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5flm

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2668

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