+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10438 | ||||||||||||
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Title | Structure of SAGA bound to TBP | ||||||||||||
Map data | SAGA-TBP structure refined in CryoSparc | ||||||||||||
Sample |
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Function / homology | Function and homology information regulation of cellular biosynthetic process / regulation of primary metabolic process / RNA polymerase I transcription regulator complex / positive regulation of DNA-templated transcription initiation / : / RNA polymerase III type 3 promoter sequence-specific DNA binding / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...regulation of cellular biosynthetic process / regulation of primary metabolic process / RNA polymerase I transcription regulator complex / positive regulation of DNA-templated transcription initiation / : / RNA polymerase III type 3 promoter sequence-specific DNA binding / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / transcription initiation at RNA polymerase I promoter / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / DNA-templated transcription initiation / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / molecular adaptor activity / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Komagataella phaffii GS115 (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) / Yeast (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Papai G / Frechard A / Kolesnikova O / Crucifix C / Schultz P / Ben-Shem A | ||||||||||||
Funding support | France, 3 items
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Citation | Journal: Nature / Year: 2020 Title: Structure of SAGA and mechanism of TBP deposition on gene promoters. Authors: Gabor Papai / Alexandre Frechard / Olga Kolesnikova / Corinne Crucifix / Patrick Schultz / Adam Ben-Shem / Abstract: SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to ...SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes. Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 Å resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression. | ||||||||||||
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_10438.map.gz | 483.1 MB | EMDB map data format | |
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Header (meta data) | emd-10438-v30.xml emd-10438.xml | 39 KB 39 KB | Display Display | EMDB header |
Images | emd_10438.png | 148.4 KB | ||
Masks | emd_10438_msk_1.map | 512 MB | Mask map | |
Others | emd_10438_half_map_1.map.gz emd_10438_half_map_2.map.gz | 474.7 MB 474.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10438 | HTTPS FTP |
-Related structure data
Related structure data | 6tb4MC 6tbmC 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_10438.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SAGA-TBP structure refined in CryoSparc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10438_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half B map obtained with CryoSparc
File | emd_10438_half_map_1.map | ||||||||||||
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Annotation | Half B map obtained with CryoSparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10438_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SAGA bound to TBP
+Supramolecule #1: SAGA bound to TBP
+Supramolecule #2: TATA-box Binding Protein (TBP)
+Supramolecule #3: SAGA complex
+Macromolecule #1: TATA-box Binding Protein (TBP)
+Macromolecule #2: Transcriptional coactivator HFI1/ADA1
+Macromolecule #3: SAGA-associated factor 73 (Sgf73)
+Macromolecule #4: Spt20
+Macromolecule #5: Subunit of the SAGA and SAGA-like transcriptional regulatory comp...
+Macromolecule #6: Subunit of the SAGA transcriptional regulatory complex, involved ...
+Macromolecule #7: Transcription initiation factor TFIID subunit 10
+Macromolecule #8: Subunit (61/68 kDa) of TFIID and SAGA complexes
+Macromolecule #9: Subunit (90 kDa) of TFIID and SAGA complexes
+Macromolecule #10: Subunit (60 kDa) of TFIID and SAGA complexes
+Macromolecule #11: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA pol...
+Macromolecule #12: Transcription-associated protein
+Macromolecule #13: Transcriptional adapter 3 (Ada3)
-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: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.0045000000000000005 µm / Calibrated defocus min: 0.0008 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 52.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1068534 |
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CTF correction | Software - Name: Warp |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354104 |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-6tb4: |