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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31114 | |||||||||
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Title | TFIID in canonical conformation | |||||||||
![]() | TFIID in canonical conformation | |||||||||
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Function / homology | ![]() 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 / negative regulation of cell cycle / P-TEFb complex binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA polymerase II general transcription initiation factor activity / 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 / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / 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 receptor binding / nuclear estrogen 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31 KB 31 KB | Display Display | ![]() |
Images | ![]() | 77.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 310.9 KB | Display | ![]() |
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Full document | ![]() | 310.5 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7egeMC ![]() 7edxC ![]() 7eg7C ![]() 7eg8C ![]() 7eg9C ![]() 7egaC ![]() 7egbC ![]() 7egcC ![]() 7egdC ![]() 7egfC ![]() 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 in canonical conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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 in canonical conformation
+Supramolecule #1: TFIID in canonical conformation
+Macromolecule #1: Transcription initiation factor TFIID subunit 1
+Macromolecule #2: Transcription initiation factor TFIID subunit 2
+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 7
+Macromolecule #7: Transcription initiation factor TFIID subunit 8
+Macromolecule #8: Transcription initiation factor TFIID subunit 9
+Macromolecule #9: Transcription initiation factor TFIID subunit 10
+Macromolecule #10: Transcription initiation factor TFIID subunit 12
+Macromolecule #11: TATA-box-binding protein
+Macromolecule #12: Transcription initiation factor TFIID subunit 3
+Macromolecule #13: Transcription initiation factor TFIID subunit 11
+Macromolecule #14: 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 | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66920 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7ege: |