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- EMDB-31118: TFIID in rearranged conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-31118
TitleTFIID in rearranged conformationTranscription factor II D
Map data
SampleTFIID in rearranged conformationTranscription factor II D
  • (Transcription initiation factor TFIID subunit ...) x 13
  • (Transcription initiation factor IIA subunit ...) x 2
  • TATA-box-binding protein
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / pre-snoRNP complex / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / STAGA complex / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / transcription factor TFTC complex ...spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / pre-snoRNP complex / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / STAGA complex / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / PCAF complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / regulation of DNA binding / transcription regulator inhibitor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 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 / 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 / transcription factor catabolic process / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / negative regulation of histone acetylation / C2H2 zinc finger domain binding / positive regulation by host of viral transcription / male pronucleus / female pronucleus / RNA polymerase binding / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / vitamin D receptor binding / midbrain development / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase I transcription / regulation of fat cell differentiation / positive regulation of gene expression, epigenetic / RNA polymerase II general transcription initiation factor activity / snRNA transcription by RNA polymerase II / cellular response to ATP / transcription factor TFIID complex / ubiquitin conjugating enzyme activity / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of transcription initiation from RNA polymerase II promoter / cellular protein-containing complex assembly / MLL1 complex / negative regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / TFIIB-class transcription factor binding / transcription by RNA polymerase III / P-TEFb complex binding / RNA Polymerase II Pre-transcription Events / transcription preinitiation complex / negative regulation of ubiquitin-dependent protein catabolic process / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase binding / intracellular estrogen receptor signaling pathway / ovarian follicle development / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / histone acetylation / core promoter sequence-specific DNA binding / DNA-binding transcription factor binding => GO:0140297 / DNA-binding transcription factor binding => GO:0140297 / histone acetyltransferase activity / histone acetyltransferase / SIRT1 negatively regulates rRNA expression / histone H3 acetylation / aryl hydrocarbon receptor binding / euchromatin / positive regulation of intrinsic apoptotic signaling pathway / TBP-class protein binding / response to interleukin-1 / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / nuclear receptor binding => GO:0016922 / promoter-specific chromatin binding / DNA-templated transcription, initiation / B-WICH complex positively regulates rRNA expression
Similarity search - Function
TAFII28-like protein / hTAFII28-like protein conserved region / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein, conserved region / 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 ...TAFII28-like protein / hTAFII28-like protein conserved region / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein, conserved region / 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. / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAF homology / Transcription initiation factor IID, 31kD subunit / Bromodomain associated domain / TAFH/NHR1 / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 6 / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 12 domain / TATA box-binding protein binding / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID, 23-30kDa subunit / Transcription initiation factor TFIID subunit 1, domain of unknown function / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription factor IIA, beta-barrel / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit / LIS1 homology (LisH) motif profile. / LIS1 homology motif / TATA-box binding protein, eukaryotic / TATA-box binding protein, conserved site / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / Aminopeptidase N-like , N-terminal / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / PHD-finger / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone-fold / PHD zinc finger / Zinc finger, PHD-type / G-protein beta WD-40 repeat / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Bromodomain / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain / Bromodomain profile. / WD40 repeats / bromo domain / Bromodomain / WD40 repeat / Bromodomain-like superfamily / WD40-repeat-containing domain superfamily / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 10 ...Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor TFIID subunit 1 / TATA-box-binding protein / Transcription initiation factor TFIID subunit 4 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.82 Å
AuthorsChen X / Wu Z / Li J / Zhao D / 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 12, 2021-
Map releaseMay 12, 2021-
UpdateMay 12, 2021-
Current statusMay 12, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7egi
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31118.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 320 pix.
= 432. Å
1.35 Å/pix.
x 320 pix.
= 432. Å
1.35 Å/pix.
x 320 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.012188528 - 0.03969783
Average (Standard dev.)0.00033034253 (±0.002271909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0120.0400.000

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Supplemental data

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Sample components

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Entire TFIID in rearranged conformation

EntireName: TFIID in rearranged conformationTranscription factor II D
Number of components: 17

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Component #1: protein, TFIID in rearranged conformation

ProteinName: TFIID in rearranged conformationTranscription factor II D
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: 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 #3: 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 #4: 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 #5: 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 #6: 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 #7: 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 #8: 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 #9: 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: 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 #17: 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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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 64496
3D reconstructionResolution: 9.82 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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