+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12897 | |||||||||
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Title | Nucleosome with TBP and TFIIA bound at SHL -6 | |||||||||
Map data | 3D refinement map from Relion | |||||||||
Sample |
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Keywords | DNA binding protein nucleosome / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information transcription factor TFIIA complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / Estrogen-dependent gene expression / positive regulation of transcription initiation by RNA polymerase II ...transcription factor TFIIA complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / Estrogen-dependent gene expression / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / structural constituent of chromatin / nucleosome / nucleosome assembly / transcription by RNA polymerase II / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Wang H / Cramer P | |||||||||
Funding support | Germany, European Union, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structures and implications of TBP-nucleosome complexes. Authors: Haibo Wang / Le Xiong / Patrick Cramer / Abstract: The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at gene promoters. TBP binds and ...The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at gene promoters. TBP binds and bends DNA, and directs adjacent binding of the transcription factors TFIIA and TFIIB for PIC assembly. Here, we show that yeast TBP can bind to a nucleosome containing the Widom-601 sequence and that TBP-nucleosome binding is stabilized by TFIIA. We determine three cryo-electron microscopy (cryo-EM) structures of TBP-nucleosome complexes, two of them containing also TFIIA. TBP can bind to superhelical location (SHL) -6, which contains a TATA-like sequence, but also to SHL +2, which is GC-rich. Whereas binding to SHL -6 can occur in the absence of TFIIA, binding to SHL +2 is only observed in the presence of TFIIA and goes along with detachment of upstream terminal DNA from the histone octamer. TBP-nucleosome complexes are sterically incompatible with PIC assembly, explaining why a promoter nucleosome generally impairs transcription and must be moved before initiation can occur. | |||||||||
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_12897.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-12897-v30.xml emd-12897.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12897_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_12897.png | 178.1 KB | ||
Filedesc metadata | emd-12897.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12897 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12897 | HTTPS FTP |
-Validation report
Summary document | emd_12897_validation.pdf.gz | 421.4 KB | Display | EMDB validaton report |
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Full document | emd_12897_full_validation.pdf.gz | 421 KB | Display | |
Data in XML | emd_12897_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | emd_12897_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12897 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12897 | HTTPS FTP |
-Related structure data
Related structure data | 7oh9MC 7ohaC 7ohbC 7ohcC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12897.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D refinement map from Relion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : Nucleosome with TBP and TFIIA
+Supramolecule #1: Nucleosome with TBP and TFIIA
+Supramolecule #2: Histone octamer
+Supramolecule #3: DNA (145-MER)
+Supramolecule #4: TBP
+Supramolecule #5: TFIIA
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: TATA-binding protein
+Macromolecule #8: Transcription initiation factor IIA large subunit
+Macromolecule #9: Transcription initiation factor IIA subunit 2
+Macromolecule #5: DNA (145-MER)
+Macromolecule #6: DNA (145-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.12 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7oh9: |