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- PDB-7ege: TFIID in canonical conformation -

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Entry
Database: PDB / ID: 7ege
TitleTFIID in canonical conformation
Components
  • (Transcription initiation factor TFIID subunit ...) x 13
  • TATA-box-binding protein
KeywordsTRANSLATION / TFIID / preinitiation complex / core promoter / transcription initiation
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process ...spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / negative regulation of protein autoubiquitination / 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 / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / TFIIH-class transcription factor complex binding / hepatocyte differentiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / positive regulation of response to cytokine stimulus / positive regulation of androgen receptor activity / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / male pronucleus / female pronucleus / positive regulation by host of viral transcription / transcription regulator inhibitor activity / nuclear vitamin D receptor binding / RNA polymerase binding / box C/D snoRNP assembly / RNA polymerase II general transcription initiation factor binding / SAGA complex / limb development / regulation of fat cell differentiation / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / inner cell mass cell proliferation / response to L-glutamate / cellular response to ATP / midbrain development / histone acetyltransferase binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / regulation of RNA splicing / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / MLL1 complex / transcription factor TFIID complex / TFIIB-class transcription factor binding / P-TEFb complex binding / negative regulation of cell cycle / RNA polymerase II general transcription initiation factor activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / estrogen receptor signaling pathway / regulation of DNA repair / somitogenesis / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / nuclear receptor binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / euchromatin / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression
Similarity search - Function
TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / 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 initiation factor TFIID subunit 8 / Transcription initiation factor TFIID component TAF4 ...TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / 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 initiation factor TFIID subunit 8 / Transcription initiation factor TFIID component TAF4 / 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 TFIID component TAF4, C-terminal / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / 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 / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / LIS1 homology (LisH) motif profile. / LIS1 homology motif / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Aminopeptidase N-like , N-terminal domain superfamliy / TBP domain superfamily / Peptidase M4/M1, CTD superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 4 / TATA-box-binding protein / Transcription initiation factor TFIID subunit 1 / 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 7 / Transcription initiation factor TFIID subunit 12 ...Transcription initiation factor TFIID subunit 4 / TATA-box-binding protein / Transcription initiation factor TFIID subunit 1 / 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 7 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 3 / 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: 9 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
D: Transcription initiation factor TFIID subunit 4
E: Transcription initiation factor TFIID subunit 5
F: Transcription initiation factor TFIID subunit 6
G: Transcription initiation factor TFIID subunit 7
H: Transcription initiation factor TFIID subunit 8
I: Transcription initiation factor TFIID subunit 9
J: Transcription initiation factor TFIID subunit 10
L: Transcription initiation factor TFIID subunit 12
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)1,281,07220
Polymers1,281,07220
Non-polymers00
Water00
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 ... , 13 types, 19 molecules ABDdEeFfGHIiJjLlckm

#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 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.: 2
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.: 2
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.: 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
#6: 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
#7: 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
#8: 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.: 2
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
#9: 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.: 2
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
#10: 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.: 2
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
#12: 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
#13: 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
#14: 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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Protein , 1 types, 1 molecules P

#11: 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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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 in canonical conformation / Type: COMPLEX / Entity ID: all / 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 / Grid type: Quantifoil R1.2/1.3
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 FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder 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: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66920 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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