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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31115 | |||||||||
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Title | TFIID lobe A subcomplex | |||||||||
![]() | TFIID lobe A subcomplex | |||||||||
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![]() | TFIID / preinitiation complex / core promoter / transcription initiation / TRANSCRIPTION | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
![]() | Chen X / Wu Z | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.7 KB 23.7 KB | Display Display | ![]() |
Images | ![]() | 13.5 KB | ||
Filedesc metadata | ![]() | 8.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7egfMC ![]() 7edxC ![]() 7eg7C ![]() 7eg8C ![]() 7eg9C ![]() 7egaC ![]() 7egbC ![]() 7egcC ![]() 7egdC ![]() 7egeC ![]() 7eggC ![]() 7eghC ![]() 7egiC ![]() 7egjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | TFIID lobe A subcomplex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : TFIID lobe A subcomplex
+Supramolecule #1: TFIID lobe A subcomplex
+Macromolecule #1: TATA-box-binding protein
+Macromolecule #2: Transcription initiation factor TFIID subunit 3
+Macromolecule #3: Transcription initiation factor TFIID subunit 4
+Macromolecule #4: Transcription initiation factor TFIID subunit 5
+Macromolecule #5: Transcription initiation factor TFIID subunit 6
+Macromolecule #6: Transcription initiation factor TFIID subunit 9
+Macromolecule #7: Transcription initiation factor TFIID subunit 10
+Macromolecule #8: Transcription initiation factor TFIID subunit 11
+Macromolecule #9: Transcription initiation factor TFIID subunit 12
+Macromolecule #10: Transcription initiation factor TFIID subunit 13
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15078 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7egf: |