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- EMDB-31111: TFIID-based holo PIC on SCP promoter -

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Basic information

Entry
Database: EMDB / ID: EMD-31111
TitleTFIID-based holo PIC on SCP promoter
Map data
SampleTFIID-based holo PIC on SCP promoter
  • TFIIDTranscription factor II D
  • RNA POLYMERASE II
  • TFIIATranscription factor II A
  • TFIIBTranscription factor II B
  • TFIIFTranscription factor II F
  • DNA(SCP promoters)
  • TFIIHTranscription factor II H
  • CDK-activating kinase assembly factor MAT1
  • (General transcription factor IIH subunit ...) x 5
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • Cyclin-dependent kinase 7
  • Cyclin-H
  • (Transcription initiation factor ...) x 17
  • TATA-box-binding protein
  • (General transcription factor IIF subunit ...) x 2
  • General transcription factor IIE subunit 1
  • (nucleic-acidNucleic acid) x 2
  • (DNA-directed RNA ...) x 9
  • RPB10
  • RNA_pol_L_2 domain-containing protein
  • RPB12
  • (ligand) x 3
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / spermine transport / negative regulation of MHC class I biosynthetic process / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly ...cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / spermine transport / negative regulation of MHC class I biosynthetic process / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / TFIIH-class transcription factor complex binding / transcription factor TFIIK complex / pre-snoRNP complex / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / positive regulation of mitotic recombination / SAGA complex => GO:0000124 / RNA polymerase II core complex assembly / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / Transcriptional regulation by small RNAs / RNA polymerase II transcribes snRNA genes / mRNA Capping / Formation of RNA Pol II elongation complex / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / 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 / RNA Polymerase II Promoter Escape / Estrogen-dependent gene expression / adult heart development / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / hair cell differentiation / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / nucleotide-excision repair factor 3 complex / negative regulation of MHC class II biosynthetic process / embryonic cleavage / SAGA complex => GO:0000124 / transcription factor TFIIE complex / regulation of cell cycle G1/S phase transition / phosphatase activator activity / TFIIF-class transcription factor complex binding / negative regulation of DNA helicase activity / [RNA-polymerase]-subunit kinase / SLIK (SAGA-like) complex / positive regulation of core promoter binding / RNA polymerase I general transcription initiation factor activity / transcription factor TFIIH core complex / UV protection / transcription factor TFIIH holo complex / regulation of DNA binding / transcription factor TFIIF complex / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / transcription regulator inhibitor activity / transcription elongation from RNA polymerase I promoter / G protein-coupled receptor internalization / SAGA complex / RNA Polymerase III Transcription Initiation From Type 3 Promoter / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II-specific DNA-binding transcription factor binding / phosphorylation of RNA polymerase II C-terminal domain / maintenance of protein location in nucleus / RNA polymerase III general transcription initiation factor activity / histone deubiquitination / hepatocyte differentiation / transcription factor TFIIA complex / positive regulation of androgen receptor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / 5'-3' DNA helicase activity / RNA polymerase II general transcription initiation factor binding / transcription factor catabolic process / negative regulation of histone acetylation / box C/D snoRNP assembly / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / positive regulation by host of viral transcription / RNA Pol II CTD phosphorylation and interaction with CE / C2H2 zinc finger domain binding / FGFR2 alternative splicing / male pronucleus / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex
Similarity search - Function
CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / hTAFII28-like protein conserved region / TAFII28-like protein domain / TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region ...CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / hTAFII28-like protein conserved region / TAFII28-like protein domain / TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription factor TFIID complex subunit 8 C-term / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor TFIID component TAF4, C-terminal / Bromodomain associated / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / Bromodomain transcription factors and PHD domain containing proteins / TAFH/NHR1 domain superfamily / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Cdk-activating kinase assembly factor MAT1, centre / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TAFH/NHR1 / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1/Tfb3 / CDK-activating kinase assembly factor MAT1 / TFIID subunit TAF5, NTD2 domain superfamily / C-terminal general transcription factor TFIIE alpha / WD40 associated region in TFIID subunit, NTD2 domain / Transcription factor TFIIE alpha subunit, C-terminal / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / TAF6, C-terminal HEAT repeat domain / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / Ssl1-like / TFIIH subunit Tfb1/GTF2H1 / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal domain / TFIIH C1-like domain / Ssl1-like / RAD3/XPD family / TFIIH subunit Ssl1/p44 / TFIIH p62 subunit, N-terminal / BSD domain / domain in transcription factors and synapse-associated proteins / BSD domain / Transcription initiation factor TFIID 23-30kDa subunit / BSD domain profile. / Transcription initiation factor TFIID, 23-30kDa subunit / Helical and beta-bridge domain / Helical and beta-bridge domain / TATA box-binding protein binding / TAFII-230 TBP-binding domain superfamily / ATP-dependent helicase Rad3/Chl1-like / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding / Helicase conserved C-terminal domain / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2 / Zinc knuckle / Transcription factor Tfb2, C-terminal domain / Zinc knuckle / ERCC3/RAD25/XPB helicase, C-terminal domain / Transcription initiation factor TFIID subunit 1, domain of unknown function / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID subunit 1 / ERCC3/RAD25/XPB C-terminal helicase / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / TFIIH subunit TTDA/Tfb5 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD2 / DEXDc2 / HELICc2 / Helicase-like, DEXD box c2 type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEAD_2 / TFA2 Winged helix domain 2 / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2
Similarity search - Domain/homology
General transcription factor IIH subunit 3 / 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 / Transcription initiation factor TFIID subunit 10 / General transcription factor IIH subunit 2 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 5 ...General transcription factor IIH subunit 3 / 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 / Transcription initiation factor TFIID subunit 10 / General transcription factor IIH subunit 2 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 12 / Cyclin-dependent kinase 7 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 2 / General transcription factor IIH subunit 5 / Transcription initiation factor TFIID subunit 8 / Cyclin-H / DNA-directed RNA polymerase II subunit RPB1 / Transcription initiation factor TFIID subunit 6 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / Uncharacterized protein / DNA-directed RNA polymerase subunit beta / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit E / Transcription initiation factor TFIID subunit 4 / General transcription factor IIF subunit 1 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / TATA-box-binding protein / Transcription initiation factor TFIID subunit 1 / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIH subunit 1 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Human (human) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen X / Wu Z / Hou H / Qi Y / Wang X / Li J / Xu Y
CitationJournal: Science / Year: 2021
Title: Structural insights into preinitiation complex assembly on core promoters.
Authors: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu /
Abstract: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
History
DepositionMar 24, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7egb
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7egb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31111.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å
1.06 Å/pix.
x 512 pix.
= 542.72 Å
1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-4.3819532 - 6.8105483
Average (Standard dev.)-0.00034348344 (±0.08411277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z542.720542.720542.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-4.3826.811-0.000

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Supplemental data

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Additional map: 3.4 Angstrom TBP module

Fileemd_31111_additional_1.map
Annotation3.4 Angstrom TBP module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: 3.4 Angstrom TBP module

Fileemd_31111_additional_2.map
Annotation3.4 Angstrom TBP module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire TFIID-based holo PIC on SCP promoter

EntireName: TFIID-based holo PIC on SCP promoter / Number of Components: 56

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Component #1: protein, TFIID-based holo PIC on SCP promoter

ProteinName: TFIID-based holo PIC on SCP promoter / Recombinant expression: No

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Component #2: protein, TFIID

ProteinName: TFIIDTranscription factor II D / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK239T

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Component #3: protein, RNA POLYMERASE II

ProteinName: RNA POLYMERASE II / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #4: protein, TFIIA

ProteinName: TFIIATranscription factor II A / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #5: protein, TFIIB

ProteinName: TFIIBTranscription factor II B / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #6: protein, TFIIF

ProteinName: TFIIFTranscription factor II F / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #7: protein, DNA(SCP promoters)

ProteinName: DNA(SCP promoters) / Recombinant expression: No

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Component #8: protein, TFIIH

ProteinName: TFIIHTranscription factor II H / Recombinant expression: No

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Component #9: 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: Homo sapiens (human)

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Component #10: 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: Homo sapiens (human)

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Component #11: 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: Homo sapiens (human)

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Component #12: 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: Homo sapiens (human)

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Component #13: 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: Homo sapiens (human)

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Component #14: 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: Homo sapiens (human)

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Component #15: 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: Homo sapiens (human)

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Component #16: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPD
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.021078 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #17: protein, Cyclin-dependent kinase 7

ProteinName: Cyclin-dependent kinase 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.090344 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #18: protein, Cyclin-H

ProteinName: Cyclin-H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.695473 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #19: protein, Transcription initiation factor TFIID subunit 1

ProteinName: Transcription initiation factor TFIID subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 212.956172 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #20: protein, Transcription initiation factor TFIID subunit 2

ProteinName: Transcription initiation factor TFIID subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.159984 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #21: protein, Transcription initiation factor TFIID subunit 4

ProteinName: Transcription initiation factor TFIID subunit 4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 110.221883 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #22: protein, Transcription initiation factor TFIID subunit 5

ProteinName: Transcription initiation factor TFIID subunit 5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 86.932109 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #23: protein, Transcription initiation factor TFIID subunit 6

ProteinName: Transcription initiation factor TFIID subunit 6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 72.749297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #24: protein, Transcription initiation factor TFIID subunit 7

ProteinName: Transcription initiation factor TFIID subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.325117 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #25: protein, Transcription initiation factor TFIID subunit 8

ProteinName: Transcription initiation factor TFIID subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.304359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #26: protein, Transcription initiation factor TFIID subunit 9

ProteinName: Transcription initiation factor TFIID subunit 9 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.006838 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #27: protein, Transcription initiation factor TFIID subunit 10

ProteinName: Transcription initiation factor TFIID subunit 10 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.731248 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #28: protein, Transcription initiation factor TFIID subunit 12

ProteinName: Transcription initiation factor TFIID subunit 12 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.948467 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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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: Homo sapiens (human)

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Component #30: 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: Homo sapiens (human)

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Component #31: 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: Homo sapiens (human)

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Component #32: 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: Homo sapiens (human)

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Component #33: 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: Homo sapiens (human)

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Component #34: 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: Homo sapiens (human)

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Component #35: 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: Homo sapiens (human)

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Component #36: 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: Homo sapiens (human)

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Component #37: nucleic-acid, DNA (69-MER)

nucleic acidName: DNA (69-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DC) (DG)(DC)(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)(DG) ...Sequence:
(DA)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DC) (DG)(DC)(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)(DG)(DT)(DC)(DG)(DC) (DG)(DA)(DT)(DC)(DG)(DA)(DA)(DC)(DA)(DC) (DT)(DC)(DG)(DA)(DG)(DC)(DC)(DG)(DA)(DG) (DC)(DA)(DG)(DA)(DC)(DG)(DT)(DG)(DC)(DC) (DT)(DA)(DC)(DG)(DG)(DA)(DC)(DC)(DA)(DT) (DG)(DG)(DA)(DT)
MassTheoretical: 29.188615 kDa
SourceSpecies: Homo sapiens (human)

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Component #38: nucleic-acid, DNA (69-MER)

nucleic acidName: DNA (69-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG)(DC)(DT) (DC)(DG)(DA)(DG)(DT)(DG)(DT)(DT)(DC)(DG) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DT)(DG) (DA)(DG)(DG)(DA)(DC)(DG)(DA)(DA)(DC)(DG) (DC)(DG)(DC)(DC)(DC)(DC) ...Sequence:
(DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG)(DC)(DT) (DC)(DG)(DA)(DG)(DT)(DG)(DT)(DT)(DC)(DG) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(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)(DG)(DC)(DG)(DC)(DC)(DC)(DT)(DT)
MassTheoretical: 21.094428 kDa
SourceSpecies: Homo sapiens (human)

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Component #39: protein, Transcription initiation factor TFIID subunit 3

ProteinName: Transcription initiation factor TFIID subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.76932 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #40: protein, Transcription initiation factor TFIID subunit 11

ProteinName: Transcription initiation factor TFIID subunit 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.340094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #41: protein, Transcription initiation factor TFIID subunit 13

ProteinName: Transcription initiation factor TFIID subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.307068 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #42: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.420047 kDa
SourceSpecies: Human (human)

+
Component #43: 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)

+
Component #44: 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)

+
Component #45: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Pig (pig)

+
Component #46: 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)

+
Component #47: 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)

+
Component #48: 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)

+
Component #49: 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)

+
Component #50: 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)

+
Component #51: protein, RPB10

ProteinName: RPB10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Pig (pig)

+
Component #52: 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)

+
Component #53: protein, RPB12

ProteinName: RPB12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Pig (pig)

+
Component #54: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #55: ligand, IRON/SULFUR CLUSTER

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

+
Component #56: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationCryogen Name: ETHANE

-
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: 50 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 92806
3D reconstructionResolution: 3.3 Å / Resolution Method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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