+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0249 | |||||||||
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Title | Structure of K. phaffii TFIID | |||||||||
Map data | komagataella phaffii (formerly Pichia pastoris) TFIID | |||||||||
Sample |
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Biological species | Komagataella phaffii GS115 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.13 Å | |||||||||
Authors | Kolesnikova O / Ben-Shem A / Luo J / Ranish J / Schultz P / Papai G | |||||||||
Citation | Journal: Nat Commun / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0249.map.gz | 11.5 MB | EMDB map data format | |
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Header (meta data) | emd-0249-v30.xml emd-0249.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0249_fsc.xml | 6.7 KB | Display | FSC data file |
Images | emd_0249.png | 84.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0249 | HTTPS FTP |
-Validation report
Summary document | emd_0249_validation.pdf.gz | 237.7 KB | Display | EMDB validaton report |
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Full document | emd_0249_full_validation.pdf.gz | 236.8 KB | Display | |
Data in XML | emd_0249_validation.xml.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0249 | HTTPS FTP |
-Related structure data
Related structure data | 0250C 0251C 0253C 0254C 0255C 6hqaC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0249.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | komagataella phaffii (formerly Pichia pastoris) TFIID | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 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 : Transcription Factor IID
Entire | Name: Transcription Factor IID |
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Components |
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-Supramolecule #1: Transcription Factor IID
Supramolecule | Name: Transcription Factor IID / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Komagataella phaffii GS115 (fungus) |
Molecular weight | Theoretical: 900 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / 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 |
Details | Monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Cs corrector is present on the microscope |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Average exposure time: 1.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.322 µm / Calibrated defocus min: 0.85 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |