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- PDB-7egf: TFIID lobe A subcomplex -

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Basic information

Entry
Database: PDB / ID: 7egf
TitleTFIID lobe A subcomplex
Components
  • (Transcription initiation factor TFIID subunit ...) x 9
  • TATA-box-binding protein
KeywordsTRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation
Function / homology
Function and homology information


pre-snoRNP complex / STAGA complex / transcription factor TFTC complex / PCAF complex / SLIK (SAGA-like) complex / regulation of DNA binding / transcription regulator inhibitor activity / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / SAGA complex ...pre-snoRNP complex / STAGA complex / transcription factor TFTC complex / PCAF complex / SLIK (SAGA-like) complex / regulation of DNA binding / transcription regulator inhibitor activity / 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 / positive regulation of response to cytokine stimulus / RNA Polymerase III Abortive And Retractive Initiation / maintenance of protein location in nucleus / 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 / RNA polymerase II general transcription initiation factor binding / 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 / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase I transcription / positive regulation of gene expression, epigenetic / RNA polymerase II general transcription initiation factor activity / snRNA transcription by RNA polymerase II / transcription factor TFIID complex / 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 / RNA Polymerase II Pre-transcription Events / transcription preinitiation complex / RNA polymerase II core promoter sequence-specific DNA binding / 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 / 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 / promoter-specific chromatin binding / DNA-templated transcription, initiation / B-WICH complex positively regulates rRNA expression / G1/S transition of mitotic cell cycle / transcription by RNA polymerase II / multicellular organism growth / estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / actin cytoskeleton / p53 binding / spermatogenesis / HATs acetylate histones / positive regulation of DNA-binding transcription factor activity / protein N-terminus binding / nuclear membrane / ATPase binding / transcription initiation from RNA polymerase II promoter / Estrogen-dependent gene expression / protein stabilization / protein C-terminus binding / Regulation of TP53 Activity through Phosphorylation / regulation of gene expression / transcription coactivator activity / regulation of signal transduction by p53 class mediator / transcription cis-regulatory region binding / Ub-specific processing proteases / protein deubiquitination / protein heterodimerization activity / negative regulation of cell population proliferation
Similarity search - Function
TAFII28-like protein / hTAFII28-like protein conserved region / 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 / Bromodomain associated / NHR1 homology to TAF / TAFH/NHR1 domain profile. / Bromodomain transcription factors and PHD domain containing proteins ...TAFII28-like protein / hTAFII28-like protein conserved region / 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 / Bromodomain associated / NHR1 homology to TAF / TAFH/NHR1 domain profile. / Bromodomain transcription factors and PHD domain containing proteins / TAF homology / TAFH/NHR1 domain superfamily / Transcription initiation factor IID, 31kD subunit / Bromodomain associated domain / Transcription initiation factor TFIID subunit A / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / 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 / Transcription initiation factor TFIID subunit 6 / TFIID subunit TAF5, NTD2 domain / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / LIS1 homology (LisH) motif profile. / LIS1 homology motif / TATA-box binding protein, eukaryotic / TATA-box binding protein, conserved site / Transcription factor TFIID repeat signature. / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / TBP domain superfamily / 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 / Zinc finger, PHD-type / PHD zinc finger / G-protein beta WD-40 repeat / Zinc finger, FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain / WD40 repeats / WD40 repeat / 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 4 / TATA-box-binding protein / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 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 5, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
P: TATA-box-binding protein
c: Transcription initiation factor TFIID subunit 3
d: Transcription initiation factor TFIID subunit 4
e: Transcription initiation factor TFIID subunit 5
f: Transcription initiation factor TFIID subunit 6
i: Transcription initiation factor TFIID subunit 9
j: Transcription initiation factor TFIID subunit 10
k: Transcription initiation factor TFIID subunit 11
l: Transcription initiation factor TFIID subunit 12
m: Transcription initiation factor TFIID subunit 13


Theoretical massNumber of molelcules
Total (without water)517,73610
Polymers517,73610
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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Protein , 1 types, 1 molecules P

#1: Protein TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation ...TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 37729.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Homo sapiens (human) / References: UniProt: P20226

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Transcription initiation factor TFIID subunit ... , 9 types, 9 molecules cdefijklm

#2: Protein Transcription initiation factor TFIID subunit 3 / 140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription ...140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / TAF(II)140 / TAF140 / TAFII-140 / TAFII140


Mass: 103769.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF3 / Production host: Homo sapiens (human) / References: UniProt: Q5VWG9
#3: Protein Transcription initiation factor TFIID subunit 4 / RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription ...RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription initiation factor TFIID 130 kDa subunit / TAF(II)130 / TAFII-130 / TAFII130 / Transcription initiation factor TFIID 135 kDa subunit / TAF(II)135 / TAFII-135 / TAFII135


Mass: 110221.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135 / Production host: Homo sapiens (human) / References: UniProt: O00268
#4: Protein Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID 100 kDa subunit / TAF(II)100 / TAFII-100 / TAFII100


Mass: 86932.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF5, TAF2D / Production host: Homo sapiens (human) / References: UniProt: Q15542
#5: 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.: 1
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
#6: Protein Transcription initiation factor TFIID subunit 9 / RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor ...RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor TFIID 31 kDa subunit / TAFII-31 / TAFII31 / Transcription initiation factor TFIID 32 kDa subunit / TAFII-32 / TAFII32


Mass: 29006.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF9, TAF2G, TAFII31 / Production host: Homo sapiens (human) / References: UniProt: Q16594
#7: Protein Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAF(II)30 / TAFII-30 / TAFII30


Mass: 21731.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF10, TAF2A, TAF2H, TAFII30 / Production host: Homo sapiens (human) / References: UniProt: Q12962
#8: Protein Transcription initiation factor TFIID subunit 11 / TFIID subunit p30-beta / Transcription initiation factor TFIID 28 kDa subunit / TAF(II)28 / TAFII-28 / TAFII28


Mass: 23340.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF11, TAF2I, PRO2134 / Production host: Homo sapiens (human) / References: UniProt: Q15544
#9: Protein Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII-20/TAFII-15 / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF12, TAF15, TAF2J, TAFII20 / Production host: Homo sapiens (human) / References: UniProt: Q16514
#10: Protein Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID 18 kDa subunit / TAF(II)18 / TAFII-18 / TAFII18


Mass: 14307.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF13, TAF2K, TAFII18 / Production host: Homo sapiens (human) / References: UniProt: Q15543

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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 A subcomplex / Type: COMPLEX / Entity ID: #1-#10 / 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
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15078 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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