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- EMDB-2229: The architecture of human general transcription factor TFIID core... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2229 | |||||||||
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Title | The architecture of human general transcription factor TFIID core complex | |||||||||
![]() | Cryo-EM structure of the recombinant human 3TAF complex | |||||||||
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![]() | human TFIID / general transcription factor / transcription / multibac / recombinant protein | |||||||||
Function / homology | ![]() transcription cis-regulatory region binding => GO:0000976 / : / modulation by virus of host process / transcription factor TFTC complex / transcription factor TFIID complex / viral process / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / actin cytoskeleton / DNA-binding transcription factor activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.8 Å | |||||||||
![]() | Bieniossek C / Papai G / Schaffitzel C / Garzoni F / Chaillet M / Scheer E / Papadopoulos P / Tora L / Schultz P / Berger I | |||||||||
![]() | ![]() Title: The architecture of human general transcription factor TFIID core complex. Authors: Christoph Bieniossek / Gabor Papai / Christiane Schaffitzel / Frederic Garzoni / Maxime Chaillet / Elisabeth Scheer / Petros Papadopoulos / Laszlo Tora / Patrick Schultz / Imre Berger / ![]() Abstract: The initiation of gene transcription by RNA polymerase II is regulated by a plethora of proteins in human cells. The first general transcription factor to bind gene promoters is transcription factor ...The initiation of gene transcription by RNA polymerase II is regulated by a plethora of proteins in human cells. The first general transcription factor to bind gene promoters is transcription factor IID (TFIID). TFIID triggers pre-initiation complex formation, functions as a coactivator by interacting with transcriptional activators and reads epigenetic marks. TFIID is a megadalton-sized multiprotein complex composed of TATA-box-binding protein (TBP) and 13 TBP-associated factors (TAFs). Despite its crucial role, the detailed architecture and assembly mechanism of TFIID remain elusive. Histone fold domains are prevalent in TAFs, and histone-like tetramer and octamer structures have been proposed in TFIID. A functional core-TFIID subcomplex was revealed in Drosophila nuclei, consisting of a subset of TAFs (TAF4, TAF5, TAF6, TAF9 and TAF12). These core subunits are thought to be present in two copies in holo-TFIID, in contrast to TBP and other TAFs that are present in a single copy, conveying a transition from symmetry to asymmetry in the TFIID assembly pathway. Here we present the structure of human core-TFIID determined by cryo-electron microscopy at 11.6 Å resolution. Our structure reveals a two-fold symmetric, interlaced architecture, with pronounced protrusions, that accommodates all conserved structural features of the TAFs including the histone folds. We further demonstrate that binding of one TAF8-TAF10 complex breaks the original symmetry of core-TFIID. We propose that the resulting asymmetric structure serves as a functional scaffold to nucleate holo-TFIID assembly, by accreting one copy each of the remaining TAFs and TBP. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
Images | ![]() | 111.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 195.9 KB | Display | ![]() |
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Full document | ![]() | 195 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the recombinant human 3TAF complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.032 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 : Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.
Entire | Name: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9. |
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Components |
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-Supramolecule #1000: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.
Supramolecule | Name: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9. type: sample / ID: 1000 / Details: The sample was fixed by GraFix. / Oligomeric state: Dimer / Number unique components: 3 |
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Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: TATA box binding protein (TBP)-associated factor 5
Macromolecule | Name: TATA box binding protein (TBP)-associated factor 5 / type: protein_or_peptide / ID: 1 / Name.synonym: TAF5 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 100 KDa |
Recombinant expression | Organism: Baculovirus EMBacY / Recombinant plasmid: pTF |
Sequence | GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: ...GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: 0016573, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process, modulation by virus of host process InterPro: WD40 repeat, LIS1 homology motif, TFIID subunit TAF5, NTD2 domain, WD40/YVTN repeat-like-containing domain superfamily, INTERPRO: IPR017986, WD40 repeat, conserved site, G-protein beta WD-40 repeat |
-Macromolecule #2: TATA box binding protein (TBP)-associated factor 6
Macromolecule | Name: TATA box binding protein (TBP)-associated factor 6 / type: protein_or_peptide / ID: 2 / Name.synonym: TAF6 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 70 KDa |
Recombinant expression | Organism: Baculovirus EMBacY / Recombinant plasmid: pTF |
Sequence | GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: ...GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: 0016573, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process, modulation by virus of host process InterPro: TATA box binding protein associated factor (TAF), histone-like fold domain, Histone-fold, TAF6, C-terminal HEAT repeat domain |
-Macromolecule #3: TATA box binding protein (TBP)-associated factor 9
Macromolecule | Name: TATA box binding protein (TBP)-associated factor 9 / type: protein_or_peptide / ID: 3 / Name.synonym: TAF9 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 32 KDa |
Recombinant expression | Organism: Baculovirus EMBacY / Recombinant plasmid: pTF |
Sequence | GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: ...GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: 0016573, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process, modulation by virus of host process InterPro: Transcription initiation factor TAFII31, Histone-fold |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Details: 50mM HEPES pH 8.0, 150mM KCl |
Grid | Details: Quantifoil 300 mesh Cu/Rh holey carbon grid R2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: 4s, blot force 5 |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Date | Sep 15, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.16 µm / Number real images: 16 / Average electron dose: 16 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 50012 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.45 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | Picking was done with e2boxer from EMAN2, first alignment cycles were done in Imagic and refinement in Spider. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic, Spider / Number images used: 11987 |