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Open data
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Basic information
Entry | Database: PDB / ID: 7egf | ||||||
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Title | TFIID lobe A subcomplex | ||||||
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![]() | TRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation | ||||||
Function / homology | ![]() SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / RNA polymerase transcription factor SL1 complex / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / hepatocyte differentiation ...SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / RNA polymerase transcription factor SL1 complex / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA 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 / 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 / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / response to L-glutamate / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / regulation of RNA splicing / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / MLL1 complex / negative regulation of cell cycle / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / somitogenesis / regulation of DNA repair / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / RNA polymerase II preinitiation complex assembly / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / mRNA transcription by RNA polymerase II / euchromatin / NoRC negatively regulates rRNA expression / multicellular organism growth / negative regulation of DNA-binding transcription factor activity / B-WICH complex positively regulates rRNA expression / G1/S transition of mitotic cell cycle / p53 binding / actin cytoskeleton / HATs acetylate histones / ATPase binding / spermatogenesis / nuclear membrane / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / Ub-specific processing proteases / chromatin remodeling / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / DNA damage response / regulation of DNA-templated transcription / chromatin Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | ||||||
![]() | Chen, X. / Wu, Z. / Li, J. / Zhao, D. / Xu, Y. | ||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 362.2 KB | Display | ![]() |
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PDB format | ![]() | 254.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 31115MC ![]() 7edxC ![]() 7eg7C ![]() 7eg8C ![]() 7eg9C ![]() 7egaC ![]() 7egbC ![]() 7egcC ![]() 7egdC ![]() 7egeC ![]() 7eggC ![]() 7eghC ![]() 7egiC ![]() 7egjC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 1 molecules P
#1: Protein | Mass: 37729.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Transcription initiation factor TFIID subunit ... , 9 types, 9 molecules cdefijklm
#2: Protein | Mass: 103769.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Protein | Mass: 110221.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 86932.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 72749.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#6: Protein | Mass: 29006.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#7: Protein | Mass: 21731.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#8: Protein | Mass: 23340.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#9: Protein | Mass: 17948.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#10: Protein | Mass: 14307.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: TFIID lobe A subcomplex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 32 |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15078 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |