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- EMDB-12630: RNA polymerase II pre-initiation complex with intermediary promot... -

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Entry
Database: EMDB / ID: EMD-12630
TitleRNA polymerase II pre-initiation complex with intermediary promoter DNA
Map dataLocal resolution filtered and sharpened map
Sample
  • Complex: RNA polymerase II pre-initiation complex with intermediary promoter DNA
Function / homology
Function and homology information


MMXD complex / core TFIIH complex portion of holo TFIIH complex / : / Cytosolic iron-sulfur cluster assembly / positive regulation of core promoter binding / central nervous system myelin formation / RNA polymerase II core complex assembly / positive regulation of mitotic recombination / transcription factor TFIIE complex / hair cell differentiation ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / : / Cytosolic iron-sulfur cluster assembly / positive regulation of core promoter binding / central nervous system myelin formation / RNA polymerase II core complex assembly / positive regulation of mitotic recombination / transcription factor TFIIE complex / hair cell differentiation / RNA polymerase transcription factor SL1 complex / meiotic sister chromatid cohesion / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / hair follicle maturation / ventricular system development / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / transcription factor TFIIK complex / CAK-ERCC2 complex / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / transcription factor TFIIF complex / embryonic cleavage / female germ cell nucleus / 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 / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / transcription factor TFIIA complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / UV protection / RNA Polymerase III Abortive And Retractive Initiation / regulation of cyclin-dependent protein serine/threonine kinase activity / male pronucleus / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / DNA 5'-3' helicase / RNA polymerase II general transcription initiation factor binding / germinal vesicle / G protein-coupled receptor internalization / adult heart development / nuclear thyroid hormone receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / protein acetylation / transcription factor TFIID complex / cell division site / regulation of mitotic cell cycle phase transition / RNA polymerase II general transcription initiation factor activity / erythrocyte maturation / acetyltransferase activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / spinal cord development / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / bone mineralization / mRNA Capping / organelle membrane / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / aryl hydrocarbon receptor binding / viral transcription / TFIIB-class transcription factor binding / ATPase activator activity
Similarity search - Function
Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / : / MAT1 C-terminal CAK anchor / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like ...Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / : / MAT1 C-terminal CAK anchor / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / BSD domain / Transcription initiation factor TFIIE, beta subunit / BSD domain superfamily / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / BSD domain / TFA2 Winged helix domain 2 / BSD domain profile. / TFIIE beta central core DNA-binding domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ATP-dependent helicase Rad3/Chl1-like / ERCC3/RAD25/XPB helicase, C-terminal domain / : / RNA-binding domain, S1 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Transcription factor IIA, alpha/beta subunit / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Transcription factor IIA, alpha/beta subunit / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Transcription factor IIA, alpha/beta subunit / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / Helicase/UvrB, N-terminal / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Type III restriction enzyme, res subunit / Ubiquitin interacting motif
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / TATA-box-binding protein / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / CDK-activating kinase assembly factor MAT1 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 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: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12630.png

Downloads & links

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Map

FileDownload / File: emd_12630.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered and sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-21.656096 - 23.84507
Average (Standard dev.)-0.011500316 (±0.9340804)
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-21.65623.845-0.012

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Supplemental data

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Mask #1

Fileemd_12630_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution filtered map, unsharpened

Fileemd_12630_additional_1.map
AnnotationLocal resolution filtered map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 1

Fileemd_12630_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2

Fileemd_12630_half_map_2.map
AnnotationUnfiltered half 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 : RNA polymerase II pre-initiation complex with intermediary promot...

EntireName: RNA polymerase II pre-initiation complex with intermediary promoter DNA
Components
  • Complex: RNA polymerase II pre-initiation complex with intermediary promoter DNA

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Supramolecule #1: RNA polymerase II pre-initiation complex with intermediary promot...

SupramoleculeName: RNA polymerase II pre-initiation complex with intermediary promoter DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 1.47 MDa

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13380
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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