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- EMDB-12619: RNA polymerase II pre-initiation complex with open promoter DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-12619
TitleRNA polymerase II pre-initiation complex with open promoter DNA
Map data
SampleRNA polymerase II pre-initiation complex with open promoter DNA
  • TFIIH basal transcription factor complex helicase XPD subunit
  • (General transcription ...) x 9
  • CDK-activating kinase assembly factor MAT1
  • RPB1POLR2A
  • DNA-directed RNA polymerase subunit betaPolymerase
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • RPOL4c domain-containing protein
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 2
  • RNA_pol_L_2 domain-containing protein
  • RNA polymerase II subunit K
  • (Transcription initiation factor ...) x 4
  • (nucleic-acidNucleic acid) x 2
  • TATA-box-binding protein
  • (Unassigned peptide, likely ...) x 2
  • (ligand) x 5
Function / homology
Function and homology information


RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Termination / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation ...RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Termination / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / B-WICH complex positively regulates rRNA expression / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination / transcription factor TFIIK complex / Estrogen-dependent gene expression / Processing of Capped Intron-Containing Pre-mRNA / Formation of RNA Pol II elongation complex / RNA Pol II CTD phosphorylation and interaction with CE / 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 / mRNA Splicing - Major Pathway / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / RNA polymerase II core complex assembly / adult heart development / hair cell differentiation / nucleotide-excision repair factor 3 complex / embryonic cleavage / transcription factor TFIIE complex / phosphatase activator activity / TFIIF-class transcription factor complex binding / negative regulation of DNA helicase activity / transcription factor TFIIH core complex / positive regulation of core promoter binding / transcription factor TFIIH holo complex / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / G protein-coupled receptor internalization / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription elongation from RNA polymerase I promoter / cyclin-dependent protein serine/threonine kinase activator activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / phosphorylation of RNA polymerase II C-terminal domain / RNA Polymerase III Abortive And Retractive Initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription factor TFIIA complex / 5'-3' DNA helicase activity / 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 HIV-1 Early Elongation Complex / Formation of the 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 / 3'-5' DNA helicase activity / positive regulation of viral transcription / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / bone mineralization / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / HIV Transcription Initiation / RNA Polymerase II Transcription Initiation / 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
Similarity search - Function
Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / CDK-activating kinase assembly factor MAT1 / Transcription factor Tfb4 / TFIIH p62 subunit, N-terminal domain / TFIIH subunit Tfb1/GTF2H1 / Transcription factor TFIIE alpha subunit, C-terminal / TFIIH p62 subunit, N-terminal / C-terminal general transcription factor TFIIE alpha ...Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / CDK-activating kinase assembly factor MAT1 / Transcription factor Tfb4 / TFIIH p62 subunit, N-terminal domain / TFIIH subunit Tfb1/GTF2H1 / Transcription factor TFIIE alpha subunit, C-terminal / TFIIH p62 subunit, N-terminal / C-terminal general transcription factor TFIIE alpha / TFIIH subunit Tfb4/GTF2H3 / TFIIH subunit Ssl1/p44 / TFIIH C1-like domain / BSD domain / TFIIH C1-like domain / BSD domain / BSD domain profile. / Ssl1-like / Ssl1-like / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / TFIIH C1-like domain / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / ERCC3/RAD25/XPB helicase, C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH complex subunit Tfb5 / TFB5-like superfamily / TFIIH subunit TTDA/Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / DEAD2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / DEAD_2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / TFIIE beta central core DNA-binding domain profile. / TFIIE beta subunit core domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFA2, Winged helix domain 2 / TFA2 Winged helix domain 2 / Transcription initiation factor TFIIE, beta subunit / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF, beta subunit, N-terminal / TFIIF beta subunit, HTH domain / 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 factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / TATA-box binding protein, conserved site / Transcription factor TFIID repeat signature. / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / TBP domain superfamily
Similarity search - Domain/homology
Transcription initiation factor IIA subunit 1 / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 5 / 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 ...Transcription initiation factor IIA subunit 1 / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 5 / 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 IIE subunit 1 / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB7 / TATA-box-binding protein / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / 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 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA_pol_L_2 domain-containing protein / RNA polymerase II subunit D / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Pig (pig) / Human mastadenovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 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: 6.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nw0
  • Surface level: 6.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12619.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 6.4 / Movie #1: 6.4
Minimum - Maximum-16.532072 - 31.23323
Average (Standard dev.)-0.0045797164 (±0.96741694)
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-16.53231.233-0.005

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Supplemental data

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Segmentation: #1

Fileemd_12619_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 1

Fileemd_12619_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 1

Fileemd_12619_half_map_2.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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

EntireName: RNA polymerase II pre-initiation complex with open promoter DNA
Number of components: 38

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

ProteinName: RNA polymerase II pre-initiation complex with open promoter DNA
Recombinant expression: No
MassTheoretical: 1.37 MDa

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Component #2: protein, TFIIH basal transcription factor complex helicase XPD subunit

ProteinName: TFIIH basal transcription factor complex helicase XPD subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.021078 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, General transcription factor IIH subunit 1

ProteinName: General transcription factor IIH subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.116492 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, General transcription factor IIH subunit 4

ProteinName: General transcription factor IIH subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.245156 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, CDK-activating kinase assembly factor MAT1

ProteinName: CDK-activating kinase assembly factor MAT1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.873965 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, General transcription factor IIH subunit 3

ProteinName: General transcription factor IIH subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.416008 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: protein, General transcription factor IIH subunit 5

ProteinName: General transcription factor IIH subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.060362 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, General transcription factor IIH subunit 2

ProteinName: General transcription factor IIH subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.481996 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #9: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPB
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 89.404734 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #10: protein, RPB1

ProteinName: RPB1POLR2A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.450078 kDa
SourceSpecies: Sus scrofa (pig)

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Component #11: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.041422 kDa
SourceSpecies: Pig (pig)

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Component #12: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.439074 kDa
SourceSpecies: Pig (pig)

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Component #13: protein, RPOL4c domain-containing protein

ProteinName: RPOL4c domain-containing protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Pig (pig)

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Component #14: protein, DNA-directed RNA polymerase II subunit E

ProteinName: DNA-directed RNA polymerase II subunit EPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.644318 kDa
SourceSpecies: Pig (pig)

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Component #15: protein, DNA-directed RNA polymerase II subunit F

ProteinName: DNA-directed RNA polymerase II subunit FPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.477001 kDa
SourceSpecies: Pig (pig)

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Component #16: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Pig (pig)

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Component #17: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Pig (pig)

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Component #18: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.541221 kDa
SourceSpecies: Pig (pig)

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Component #19: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Pig (pig)

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Component #20: protein, RNA_pol_L_2 domain-containing protein

ProteinName: RNA_pol_L_2 domain-containing protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Pig (pig)

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Component #21: protein, RNA polymerase II subunit K

ProteinName: RNA polymerase II subunit K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Pig (pig)

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Component #22: protein, Transcription initiation factor IIB

ProteinName: Transcription initiation factor IIB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.877949 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #23: nucleic-acid, Non-template DNA

nucleic acidName: Non-template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC) ...Sequence:
(DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT)(DC)(DC) (DT)(DC)(DA)(DC)(DT)(DC)(DT)(DC)(DT)(DT) (DC)(DC)(DG)(DC)(DA)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DG) (DG)(DC)(DC)(DA)(DG)(DC)(DT)(DG)(DT)(DT) (DG)(DG)(DG)(DG)(DT)(DG)(DA)(DG)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)
MassTheoretical: 32.911859 kDa
SourceSpecies: Human mastadenovirus C

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Component #24: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.729938 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #25: protein, General transcription factor IIF subunit 1

ProteinName: General transcription factor IIF subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.343578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #26: protein, General transcription factor IIF subunit 2

ProteinName: General transcription factor IIF subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.427309 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #27: nucleic-acid, Template DNA

nucleic acidName: Template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DA)(DT)(DG)(DC)(DG)(DG) ...Sequence:
(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DA)(DT)(DG)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DA)(DG)(DT)(DG)(DA)(DG)(DG)(DA)(DC) (DG)(DA)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DC) (DC)(DC)(DA)(DC)(DC)(DC)(DC)(DC)(DT)(DT) (DT)(DT)(DA)(DT)(DA)(DG)(DC)(DC)(DC)(DC) (DC)(DC)(DT)(DT)(DC)(DA)(DG)(DG)(DA)(DA) (DC)(DA)(DC)(DC)(DC)(DG)
MassTheoretical: 32.508752 kDa
SourceSpecies: Human mastadenovirus C

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Component #28: protein, Transcription initiation factor IIA subunit 1

ProteinName: Transcription initiation factor IIA subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.544551 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #29: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.469091 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #30: protein, General transcription factor IIE subunit 1

ProteinName: General transcription factor IIE subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.516094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #31: protein, Transcription initiation factor IIE subunit beta

ProteinName: Transcription initiation factor IIE subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.106824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #32: protein, Unassigned peptide, likely TFIIE-Beta

ProteinName: Unassigned peptide, likely TFIIE-Beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.379692 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #33: protein, Unassigned peptide, likely XPB

ProteinName: Unassigned peptide, likely XPB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.698854 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #34: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #35: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #36: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #37: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #38: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.60070000000000105 MDa

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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: 26146
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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