+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10446 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SAGA-TBP filtered to show the position of the DUB domain | ||||||||||||
![]() | |||||||||||||
![]() |
| ||||||||||||
Function / homology | ![]() : / 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 / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / transcription export complex 2 / RNA polymerase I general transcription initiation factor binding / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of transcription by RNA polymerase III / 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 / mitochondrion transport along microtubule / fat pad development / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / 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 / female gonad development / RNA Polymerase II Pre-transcription Events / NuA4 histone acetyltransferase complex / seminiferous tubule development / male meiosis I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Estrogen-dependent gene expression / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / energy homeostasis / nuclear pore / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic 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 / enzyme activator activity / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TBP-class protein binding / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | ||||||||||||
![]() | Papai G / Frechard A / Kolesnikova O / Crucifix C / Schultz P / Ben-Shem A | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 53.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 45 KB 45 KB | Display Display | ![]() |
Images | ![]() | 82.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 198 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 197.2 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tbmMC ![]() 6tb4C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 2.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.4 mg/mL |
---|---|
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 |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 FIELD / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
---|---|
Output model | ![]() PDB-6tbm: |