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- EMDB-12621: Focused refinement of the core RNA polymerase II pre-initiation c... -

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Entry
Database: EMDB / ID: EMD-12621
TitleFocused refinement of the core RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3)
Map data
SampleRNA polymerase II core pre-initiation complex with open promoter DNA
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase III Transcription Initiation From Type 1 Promoter / B-WICH complex positively regulates rRNA expression / mRNA Capping / RNA polymerase II transcribes snRNA genes / FGFR2 alternative splicing / Estrogen-dependent gene expression ...RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase III Transcription Initiation From Type 1 Promoter / B-WICH complex positively regulates rRNA expression / mRNA Capping / RNA polymerase II transcribes snRNA genes / FGFR2 alternative splicing / Estrogen-dependent gene expression / TP53 Regulates Transcription of DNA Repair Genes / RNA Pol II CTD phosphorylation and interaction with CE / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / mRNA Splicing - Minor Pathway / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / mRNA Splicing - Major Pathway / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / Formation of TC-NER Pre-Incision Complex / RNA polymerase II core complex assembly / transcription factor TFIIE complex / phosphatase activator activity / TFIIF-class transcription factor complex binding / positive regulation of core promoter binding / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / nuclear-transcribed mRNA catabolic process, exonucleolytic / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / FGFR2 alternative splicing / male pronucleus / female pronucleus / Viral Messenger RNA Synthesis / mRNA export from nucleus in response to heat stress / positive regulation of viral transcription / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / Processing of Capped Intron-Containing Pre-mRNA / Transcription of the HIV genome / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / Tat-mediated HIV elongation arrest and recovery / Pausing and recovery of Tat-mediated HIV elongation / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / termination of RNA polymerase I transcription / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Signaling by FGFR2 IIIa TM / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of gene expression, epigenetic / mRNA Splicing - Minor Pathway / snRNA transcription by RNA polymerase II / RNA polymerase II general transcription initiation factor activity / RNA polymerase II activity / transcription factor TFIID complex / RNA Polymerase I Transcription Initiation / RNA metabolic process / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II transcribes snRNA genes / positive regulation of translational initiation / RNA polymerase II complex binding / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / protein acetylation / acetyltransferase activity / mRNA cleavage / TFIIB-class transcription factor binding / RNA polymerase I complex / RNA polymerase III complex
Similarity search - Function
Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFA2, Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / TFA2 Winged helix domain 2 / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFIIE beta subunit core domain / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor E ...Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFA2, Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / TFA2 Winged helix domain 2 / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFIIE beta subunit core domain / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor E / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE subunit alpha, N-terminal / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / TFIIE alpha subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit N-terminus / TFIIF, beta subunit HTH domain / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB, cyclin-like domain / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / TATA-box binding protein / Transcription factor TFIID repeat signature. / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / TBP domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit N/Rpb10 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit 9 / RNA polymerase Rpb8 / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Zinc finger, TFIIS-type / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases H / 23 Kd subunits signature.
Similarity search - Domain/homology
General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 / General transcription factor IIF subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIE subunit 1 / TATA-box-binding protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit E ...General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 / General transcription factor IIF subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIE subunit 1 / TATA-box-binding protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA_pol_L_2 domain-containing protein / RNA polymerase II subunit D / Transcription initiation factor IIB
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsAibara S / Schilbach S / Cramer P
Funding support Germany, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: Nature / Year: 2021
Title: Structures of mammalian RNA polymerase II pre-initiation complexes.
Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
History
DepositionMar 16, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 16, 2021-
Current statusJun 16, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12621.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 450 pix.
= 472.5 Å
1.05 Å/pix.
x 450 pix.
= 472.5 Å
1.05 Å/pix.
x 450 pix.
= 472.5 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
Contour LevelBy AUTHOR: 2.5 / Movie #1: 4
Minimum - Maximum-48.909164 - 80.670456
Average (Standard dev.)0.00014146138 (±0.98437464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 472.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z472.500472.500472.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-48.90980.6700.000

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Supplemental data

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Segmentation: #1

Fileemd_12621_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Additional map: Local resolution filtered map, unsharpened

Fileemd_12621_additional_1.map
AnnotationLocal resolution filtered map, unsharpened
Projections & Slices
AxesZYX

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Density Histograms

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Half map: Unfiltered half map 1

Fileemd_12621_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 2

Fileemd_12621_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire RNA polymerase II core pre-initiation complex with open promoter DNA

EntireName: RNA polymerase II core pre-initiation complex with open promoter DNA
Number of components: 1

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Component #1: protein, RNA polymerase II core pre-initiation complex with open ...

ProteinName: RNA polymerase II core pre-initiation complex with open promoter DNA
Recombinant expression: No
MassTheoretical: 880 kDa
SourceSpecies: Sus scrofa (pig)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 43 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 714395
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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