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Yorodumi- EMDB-2230: The architecture of human general transcription factor TFIID core... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2230 | |||||||||
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Title | The architecture of human general transcription factor TFIID core complex | |||||||||
Map data | Cryo-EM structure of the recombinant human core-TFIID subcomplex | |||||||||
Sample |
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Keywords | human TFIID / general transcription factor / transcription / multibac / recombinant protein | |||||||||
Function / homology | Function and homology information SAGA complex => GO:0000124 / SAGA complex => GO:0000124 / transcription cis-regulatory region binding => GO:0000976 / : / : / modulation by virus of host process / transcription factor TFTC complex / transcription factor TFIID complex / viral process / transcription initiation at RNA polymerase II promoter ...SAGA complex => GO:0000124 / SAGA complex => GO:0000124 / transcription cis-regulatory region binding => GO:0000976 / : / : / modulation by virus of host process / transcription factor TFTC complex / transcription factor TFIID complex / viral process / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / positive regulation of DNA-binding transcription factor activity / actin cytoskeleton / transcription coactivator activity / DNA-binding transcription factor activity / DNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.6 Å | |||||||||
Authors | Bieniossek C / Papai G / Schaffitzel C / Garzoni F / Chaillet M / Scheer E / Papadopoulos P / Tora L / Schultz P / Berger I | |||||||||
Citation | Journal: Nature / Year: 2013 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2230.map.gz | 290 KB | EMDB map data format | |
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Header (meta data) | emd-2230-v30.xml emd-2230.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | EMD-2230-core-TFIID-front.png | 118 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2230 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2230 | HTTPS FTP |
-Validation report
Summary document | emd_2230_validation.pdf.gz | 193.4 KB | Display | EMDB validaton report |
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Full document | emd_2230_full_validation.pdf.gz | 192.5 KB | Display | |
Data in XML | emd_2230_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2230 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2230 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2230.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the recombinant human core-TFIID subcomplex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6,...
Entire | Name: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6, TAF9 and TAF12. |
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Components |
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-Supramolecule #1000: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6,...
Supramolecule | Name: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6, TAF9 and TAF12. type: sample / ID: 1000 / Details: The sample was fixed by GraFix. / Oligomeric state: Dimer / Number unique components: 5 |
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Molecular weight | Theoretical: 700 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: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
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: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
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: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
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 |
-Macromolecule #4: TATA box binding protein (TBP)-associated factor 4
Macromolecule | Name: TATA box binding protein (TBP)-associated factor 4 / type: protein_or_peptide / ID: 4 / Name.synonym: TAF4 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
Molecular weight | Theoretical: 135 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: TAFH/NHR1, Transcription initiation factor TFIID component TAF4, C-terminal, Histone-fold |
-Macromolecule #5: TATA box binding protein (TBP)-associated factor 12
Macromolecule | Name: TATA box binding protein (TBP)-associated factor 12 / type: protein_or_peptide / ID: 5 / Name.synonym: TAF12 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
Molecular weight | Theoretical: 15 KDa |
Recombinant expression | Organism: Baculovirus EMBacY / Recombinant plasmid: pTF |
Sequence | GO: SAGA complex => GO:0000124, SAGA complex => GO:0000124, transcription factor TFIID complex, transcription factor TFTC complex, DNA binding, transcription coactivator activity, GO: 0043966, ...GO: SAGA complex => GO:0000124, SAGA complex => GO:0000124, transcription factor TFIID complex, transcription factor TFTC complex, DNA binding, transcription coactivator activity, GO: 0043966, positive regulation of DNA-binding transcription factor activity, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process InterPro: Histone-fold, Transcription initiation factor TFIID subunit 12 domain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Date | May 7, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 15.24 µm / Number real images: 23 / Average electron dose: 16 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50012 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.749 µm / Nominal defocus min: 1.851 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-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: 11.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic, Spider / Number images used: 12566 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Chain ID: D |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 4
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 5
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 6
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |