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- EMDB-31075: p53-bound TFIID-based core PIC on HDM2 promoter -

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Basic information

Entry
Database: EMDB / ID: EMD-31075
Titlep53-bound TFIID-based core PIC on HDM2 promoter
Map data
Samplep53-bound TFIID-based core PIC on HDM2 promoter
  • TFIIDTranscription factor II D
  • RNA POLYMERASE II
  • TFIIATranscription factor II A
  • TFIIBTranscription factor II B
  • TFIIFTranscription factor II F
  • DNA(SCP promoters)
  • (Transcription initiation factor TFIID subunit ...) x 13
  • (Transcription initiation factor IIA subunit ...) x 2
  • TATA-box-binding protein
  • Transcription initiation factor IIB
  • (General transcription factor IIF subunit ...) x 2
  • (nucleic-acidNucleic acid) x 2
  • RPB1POLR2A
  • (DNA-directed RNA ...) x 8
  • RPB10
  • RNA_pol_L_2 domain-containing protein
  • RPB12
  • (ligand) x 2
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / Formation of the Early Elongation Complex ...spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / mRNA Capping / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / mRNA Splicing - Major Pathway / RNA Polymerase II Transcription Initiation And Promoter Clearance / pre-snoRNP complex / mRNA Splicing - Minor Pathway / RNA Pol II CTD phosphorylation and interaction with CE / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / negative regulation of protein autoubiquitination / STAGA complex / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / RNA polymerase II core complex assembly / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / PCAF complex / regulation of cell cycle G1/S phase transition / phosphatase activator activity / TFIIF-class transcription factor complex binding / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / positive regulation of core promoter binding / regulation of DNA binding / transcription regulator inhibitor activity / transcription factor TFIIF complex / 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 / SAGA complex / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation / RNA Polymerase III Abortive And Retractive Initiation / maintenance of protein location in nucleus / positive regulation of androgen receptor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / histone deubiquitination / hepatocyte differentiation / RNA Polymerase I Transcription Termination / box C/D snoRNP assembly / general transcription initiation factor activity / transcription factor catabolic process / RNA polymerase II general transcription initiation factor binding / negative regulation of histone acetylation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the HIV-1 Early Elongation Complex / C2H2 zinc finger domain binding / Formation of the Early Elongation Complex / positive regulation by host of viral transcription / mRNA Capping / FGFR2 alternative splicing / male pronucleus / female pronucleus / Viral Messenger RNA Synthesis / positive regulation of viral transcription / RNA polymerase binding / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / Processing of Capped Intron-Containing Pre-mRNA / vitamin D receptor binding / midbrain development / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation / RNA polymerase complex / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / 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 / regulation of fat cell differentiation / termination of RNA polymerase I transcription / Pausing and recovery of HIV elongation / HIV elongation arrest and recovery / Signaling by FGFR2 IIIa TM
Similarity search - Function
hTAFII28-like protein conserved region / TAFII28-like protein / TAFII55 protein conserved region / TAFII55 protein, conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal ...hTAFII28-like protein conserved region / TAFII28-like protein / TAFII55 protein conserved region / TAFII55 protein, conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / 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 / TAFH/NHR1 domain profile. / NHR1 homology to TAF / TAF homology / TAFH/NHR1 domain superfamily / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TAFH/NHR1 / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TAF6 C-terminal HEAT repeat domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAFII-230 TBP-binding domain superfamily / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TATA box-binding protein binding / TAF6, C-terminal HEAT repeat domain / Zinc knuckle / Transcription initiation factor TFIID 23-30kDa subunit / Zinc knuckle / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 1, domain of unknown function / Transcription initiation factor TFIID, 23-30kDa subunit / TFIIF, beta subunit N-terminus / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / 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 (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB, conserved site / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein, conserved site / Transcription factor TFIID repeat signature. / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / TBP domain superfamily / Rpb4/RPC9 superfamily / Aminopeptidase N-like , N-terminal / 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 / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like / Cyclin-like superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 3 ...DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit F / Transcription initiation factor TFIID subunit 6 / General transcription factor IIF subunit 1 / Transcription initiation factor TFIID subunit 1 / TATA-box-binding protein / General transcription factor IIF subunit 2 / Transcription initiation factor TFIID subunit 4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerase subunit beta / Uncharacterized protein / DNA-directed RNA polymerase II subunit RPB4 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsChen X / Qi Y / Hou H / Wang X / Wu Z / 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 17, 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: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7edx
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7edx
  • 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_31075.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 508.8 Å
1.06 Å/pix.
x 480 pix.
= 508.8 Å
1.06 Å/pix.
x 480 pix.
= 508.8 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: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.87711555 - 1.6116302
Average (Standard dev.)0.0044647767 (±0.03306977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.8771.6120.004

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Supplemental data

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Additional map: 3.9 Angstrom TBP module

Fileemd_31075_additional_1.map
Annotation3.9 Angstrom TBP module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: 3.4 Angstrom Pol II module

Fileemd_31075_additional_2.map
Annotation3.4 Angstrom Pol II module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: 5.5 Angstrom TFIID module

Fileemd_31075_additional_3.map
Annotation5.5 Angstrom TFIID module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire p53-bound TFIID-based core PIC on HDM2 promoter

EntireName: p53-bound TFIID-based core PIC on HDM2 promoter / Number of components: 42

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Component #1: protein, p53-bound TFIID-based core PIC on HDM2 promoter

ProteinName: p53-bound TFIID-based core PIC on HDM2 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)
Source (engineered)Expression System: Sus scrofa (pig) / Cell of expression system: HEK293T

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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, 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 #9: 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: 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 #22: 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 #23: 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 #24: nucleic-acid, DNA (84-mer)

nucleic acidName: DNA (84-mer) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DC)(DT)(DG) (DG)(DG)(DG)(DC)(DT)(DA)(DT)(DT)(DT)(DA) (DA)(DA)(DC)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DG)(DT)(DG)(DT)(DT)(DC) ...Sequence:
(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DC)(DT)(DG) (DG)(DG)(DG)(DC)(DT)(DA)(DT)(DT)(DT)(DA) (DA)(DA)(DC)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DG)(DT)(DG)(DT)(DT)(DC)(DA)(DG)(DT)(DG) (DG)(DC)(DG)(DA)(DT)(DT)(DG)(DG)(DA)(DG) (DG)(DG)(DT)(DA)(DG)(DA)(DC)(DC)(DT)(DG) (DT)(DG)(DG)(DG)(DC)(DA)(DC)(DG)(DG)(DA) (DC)(DG)(DC)(DA)
MassTheoretical: 26.001576 kDa
SourceSpecies: Homo sapiens (human)

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Component #25: nucleic-acid, DNA (84-mer)

nucleic acidName: DNA (84-mer) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DG)(DC)(DG)(DT)(DC)(DC)(DG)(DT)(DG) (DC)(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DT)(DC) (DT)(DA)(DC)(DC)(DC)(DT)(DC)(DC)(DA)(DA) (DT)(DC)(DG)(DC)(DC)(DA)(DC)(DT)(DG)(DA) (DA)(DC)(DA)(DC)(DA)(DG) ...Sequence:
(DT)(DG)(DC)(DG)(DT)(DC)(DC)(DG)(DT)(DG) (DC)(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DT)(DC) (DT)(DA)(DC)(DC)(DC)(DT)(DC)(DC)(DA)(DA) (DT)(DC)(DG)(DC)(DC)(DA)(DC)(DT)(DG)(DA) (DA)(DC)(DA)(DC)(DA)(DG)(DC)(DT)(DG)(DG) (DG)(DA)(DA)(DA)(DA)(DT)(DG)(DC)(DA)(DT) (DG)(DG)(DT)(DT)(DT)(DA)(DA)(DA)(DT)(DA) (DG)(DC)(DC)(DC)(DC)(DA)(DG)(DC)(DT)(DG) (DG)(DA)(DG)(DA)
MassTheoretical: 25.815518 kDa
SourceSpecies: Homo sapiens (human)

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Component #26: 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 #27: 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)

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Component #28: 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)

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Component #29: protein, RPB1

ProteinName: RPB1POLR2A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.420047 kDa
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #30: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #31: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #32: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #33: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #34: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #35: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #36: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #37: protein, RPB10

ProteinName: RPB10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #38: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #39: protein, RPB12

ProteinName: RPB12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #40: 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: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #41: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #42: ligand, MAGNESIUM ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.9
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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 99580
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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