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- PDB-7egh: TFIID lobe C subcomplex -

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Basic information

Entry
Database: PDB / ID: 7egh
TitleTFIID lobe C subcomplex
Components
  • (DNA (45-MER)) x 2
  • (Transcription initiation factor TFIID subunit ...) x 5
KeywordsTRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / 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 / regulation of cell cycle G1/S phase transition ...spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / 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 / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / transcription regulator inhibitor activity / SAGA complex / RNA polymerase II-specific DNA-binding transcription factor binding / inner cell mass cell proliferation / maintenance of protein location in nucleus / positive regulation of androgen receptor activity / transcription factor catabolic process / negative regulation of histone acetylation / RNA polymerase II preinitiation complex assembly / transcription initiation from RNA polymerase I promoter / thyroid hormone receptor binding / vitamin D receptor binding / midbrain development / HIV Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / Transcription of the HIV genome / RNA Polymerase II HIV Promoter Escape / regulation of fat cell differentiation / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / snRNA transcription by RNA polymerase II / cellular response to ATP / ubiquitin conjugating enzyme activity / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation from RNA polymerase II promoter / MLL1 complex / negative regulation of cell cycle / P-TEFb complex binding / RNA Polymerase II Pre-transcription Events / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase binding / intracellular estrogen receptor signaling pathway / histone acetylation / histone acetyltransferase activity / histone acetyltransferase / aryl hydrocarbon receptor binding / positive regulation of intrinsic apoptotic signaling pathway / TBP-class protein binding / nuclear receptor binding => GO:0016922 / DNA-templated transcription, initiation / lysine-acetylated histone binding / response to organic cyclic compound / transcription by RNA polymerase II / cellular response to UV / negative regulation of protein kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of DNA-binding transcription factor activity / transcription regulator complex / p53 binding / peptidyl-threonine phosphorylation / protein polyubiquitination / kinase activity / G2/M transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / transcription initiation from RNA polymerase II promoter / sequence-specific DNA binding / protein stabilization / positive regulation of protein binding / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / regulation of signal transduction by p53 class mediator / transcription cis-regulatory region binding / cell cycle / non-specific serine/threonine protein kinase / cell differentiation / peptidyl-serine phosphorylation / protein kinase activity / protein heterodimerization activity / negative regulation of gene expression / protein autophosphorylation / negative regulation of cell population proliferation / positive regulation of apoptotic process / chromatin / transcription factor binding / protein serine/threonine kinase activity / cellular response to DNA damage stimulus / negative regulation of transcription, DNA-templated / protein serine kinase activity / protein threonine kinase activity / apoptotic process / chromatin binding / protein phosphorylation / regulation of transcription by RNA polymerase II / viral process
Similarity search - Function
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 / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated ...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 / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated / Bromodomain associated domain / TATA box binding protein associated factor (TAF) / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 6 / TAFII-230 TBP-binding / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Transcription initiation factor TFIID subunit 1, animal / TAF6, C-terminal HEAT repeat domain / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, domain of unknown function / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID subunit 1 / Aminopeptidase N-like , N-terminal / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone-fold / Bromodomain signature. / Bromodomain, conserved site / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
DNA (> 10) / DNA / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 2
F: Transcription initiation factor TFIID subunit 6
G: Transcription initiation factor TFIID subunit 7
H: Transcription initiation factor TFIID subunit 8
X: DNA (45-MER)
Y: DNA (45-MER)
f: Transcription initiation factor TFIID subunit 6


Theoretical massNumber of molelcules
Total (without water)621,3768
Polymers621,3768
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription initiation factor TFIID subunit ... , 5 types, 6 molecules ABFfGH

#1: Protein Transcription initiation factor TFIID subunit 1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor ...Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor TFIID 250 kDa subunit / TAF(II)250 / TAFII-250 / TAFII250


Mass: 212956.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Homo sapiens (human)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Protein Transcription initiation factor TFIID subunit 2 / 150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP- ...150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP-associated factor 150 kDa / Transcription initiation factor TFIID 150 kDa subunit / TAF(II)150 / TAFII-150 / TAFII150


Mass: 137159.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF2, CIF150, TAF2B / Production host: Homo sapiens (human) / References: UniProt: Q6P1X5
#3: Protein Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa ...RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa subunit / TAF(II)70 / TAFII-70 / TAFII70 / Transcription initiation factor TFIID 80 kDa subunit / TAF(II)80 / TAFII-80 / TAFII80


Mass: 72749.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF6, TAF2E, TAFII70 / Production host: Homo sapiens (human) / References: UniProt: P49848
#4: Protein Transcription initiation factor TFIID subunit 7 / RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa ...RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa subunit / TAF(II)55 / TAFII-55 / TAFII55


Mass: 40325.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF7, TAF2F, TAFII55 / Production host: Homo sapiens (human) / References: UniProt: Q15545
#5: Protein Transcription initiation factor TFIID subunit 8 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription ...Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription initiation factor TFIID 43 kDa subunit / TAFII-43 / TAFII43 / hTAFII43


Mass: 34304.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF8, TAFII43, TBN / Production host: Homo sapiens (human) / References: UniProt: Q7Z7C8

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DNA chain , 2 types, 2 molecules XY

#6: DNA chain DNA (45-MER)


Mass: 22317.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: DNA chain DNA (45-MER)


Mass: 28814.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TFIID lobe C subcomplex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121285 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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