+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5135 | |||||||||
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Title | TBP-lacking S. pombe TFIID | |||||||||
Map data | TBP-lacking S. pombe TFIID | |||||||||
Sample |
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Function / homology | Transcription initiation factor TFIID subunit 12 domain / transcription factor TFIID complex Function and homology information | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Elmlund H / Baraznenok V / Linder T / Szilagyi Z / Rofougaran R / Hofer A / Hebert H / Lindahl M / Gustafsson CM | |||||||||
Citation | Journal: Structure / Year: 2009 Title: Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID. Authors: Hans Elmlund / Vera Baraznenok / Tomas Linder / Zsolt Szilagyi / Reza Rofougaran / Anders Hofer / Hans Hebert / Martin Lindahl / Claes M Gustafsson / Abstract: The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and ...The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the TFIID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions. | |||||||||
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_5135.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-5135-v30.xml emd-5135.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | emd_5135_1.png | 1.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5135 | HTTPS FTP |
-Validation report
Summary document | emd_5135_validation.pdf.gz | 77.8 KB | Display | EMDB validaton report |
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Full document | emd_5135_full_validation.pdf.gz | 76.9 KB | Display | |
Data in XML | emd_5135_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5135 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5135 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5135.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TBP-lacking S. pombe TFIID | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.33 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 : Native S. pombe TFIID
Entire | Name: Native S. pombe TFIID |
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Components |
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-Supramolecule #1000: Native S. pombe TFIID
Supramolecule | Name: Native S. pombe TFIID / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 870 KDa / Theoretical: 870 KDa / Method: GEMMA |
-Macromolecule #1: TAF1-TAF12
Macromolecule | Name: TAF1-TAF12 / type: protein_or_peptide / ID: 1 / Name.synonym: TFIID / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) / synonym: Fission yeast |
Sequence | GO: transcription factor TFIID complex InterPro: 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
Vitrification | Cryogen name: METHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | JEOL 2010F |
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Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SIMPLE |
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