+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10446 | ||||||||||||
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Title | SAGA-TBP filtered to show the position of the DUB domain | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information nuclear mRNA surveillance => GO:0071028 / : / regulation of cellular biosynthetic process / regulation of primary metabolic process / SAGA-type complex / DUBm complex / : / positive regulation of DNA-templated transcription initiation / : / : ...nuclear mRNA surveillance => GO:0071028 / : / regulation of cellular biosynthetic process / regulation of primary metabolic process / SAGA-type complex / DUBm complex / : / positive regulation of DNA-templated transcription initiation / : / : / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / SLIK (SAGA-like) complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / hypothalamus gonadotrophin-releasing hormone neuron development / SAGA complex / female meiosis I / positive regulation of protein monoubiquitination / poly(A)+ mRNA export from nucleus / mitochondrion transport along microtubule / DNA binding, bending / fat pad development / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / RNA polymerase II general transcription initiation factor activity / 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 / transcription factor TFIID complex / female gonad development / RNA Polymerase II Pre-transcription Events / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / nucleolar large rRNA transcription by RNA polymerase I / enzyme activator activity / RNA polymerase II core promoter sequence-specific DNA binding / regulation of proteasomal protein catabolic process / nuclear pore / energy homeostasis / regulation of neuron apoptotic process / RNA polymerase II preinitiation complex assembly / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs Similarity search - Function | ||||||||||||
Biological species | Komagataella phaffii GS115 (fungus) / Homo sapiens (human) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) / Yeast (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 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_10446.map.gz | 53.2 MB | EMDB map data format | |
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Header (meta data) | emd-10446-v30.xml emd-10446.xml | 45 KB 45 KB | Display Display | EMDB header |
Images | emd_10446.png | 82.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10446 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10446 | HTTPS FTP |
-Related structure data
Related structure data | 6tbmMC 6tb4C C: citing same article (ref.) M: atomic model generated by this map |
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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_10446.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.18 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 : SAGA bound to TBP
+Supramolecule #1: SAGA bound to TBP
+Supramolecule #2: TATA-box binding protein (TBP)
+Supramolecule #3: SAGA component
+Supramolecule #4: Polyubiquitin-B
+Supramolecule #5: SAGA complex
+Macromolecule #1: TATA-box Binding Protein (TBP)
+Macromolecule #2: Transcriptional coactivator HFI1/ADA1
+Macromolecule #3: Subunit of SAGA histone acetyltransferase complex
+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 regulator involved in glucose repression of Gal4p...
+Macromolecule #14: Spt8
+Macromolecule #15: Polyubiquitin-B
+Macromolecule #16: Ubiquitin carboxyl-terminal hydrolase
+Macromolecule #17: SAGA-associated factor 11
+Macromolecule #18: Transcription and mRNA export factor SUS1
+Macromolecule #19: water
-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 |
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: 4.5 µm / Calibrated defocus min: 0.8 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: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 354104 |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-6tbm: |