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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0251 | ||||||||||||
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Title | Molecular structure of promoter-bound yeast TFIID | ||||||||||||
![]() | Komagataella phaffii TFIID | ||||||||||||
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Function / homology | ![]() regulation of cellular biosynthetic process / regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / SLIK (SAGA-like) complex / SAGA complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation ...regulation of cellular biosynthetic process / regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / SLIK (SAGA-like) complex / SAGA complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||||||||
![]() | Kolesnikova O / Ben-Shem A / Luo J / Ranish J / Schultz P / Papai G | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular structure of promoter-bound yeast TFIID. Authors: Olga Kolesnikova / Adam Ben-Shem / Jie Luo / Jeff Ranish / Patrick Schultz / Gabor Papai / ![]() ![]() Abstract: Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) ...Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe. | ||||||||||||
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 | ![]() | 14.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.3 KB 29.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 108.6 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() | 98.8 MB 98.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hqaMC ![]() 0249C ![]() 0250C ![]() 0253C ![]() 0254C ![]() 0255C 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 | Komagataella phaffii TFIID | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: even half map
File | emd_0251_half_map_1.map | ||||||||||||
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Annotation | even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: odd half map
File | emd_0251_half_map_2.map | ||||||||||||
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Annotation | odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Transcription Factor IID
+Supramolecule #1: Transcription Factor IID
+Macromolecule #1: Taf2
+Macromolecule #2: Subunit (90 kDa) of TFIID and SAGA complexes
+Macromolecule #3: Subunit (60 kDa) of TFIID and SAGA complexes
+Macromolecule #4: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA pol...
+Macromolecule #5: Taf8
+Macromolecule #6: Histone-fold
+Macromolecule #7: Histone-fold
+Macromolecule #8: Subunit (61/68 kDa) of TFIID and SAGA complexes
+Macromolecule #9: TFIID subunit (48 kDa)
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Equipped with Cs corrector / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 3-40 / Average exposure time: 8.0 sec. / Average electron dose: 52.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.9 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 45454 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |