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Open data
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Basic information
Entry | Database: PDB / ID: 6tbm | ||||||||||||
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Title | Structure of SAGA bound to TBP, including Spt8 and DUB | ||||||||||||
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![]() | TRANSCRIPTION / Transcriptional co-activator / Histone-acetylation | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å | ||||||||||||
![]() | Papai, G. / Frechard, A. / Kolesnikova, O. / Crucifix, C. / Schultz, P. / Ben-Shem, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 940.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 911.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 162.2 KB | Display | |
Data in CIF | ![]() | 258 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10446MC ![]() 6tb4C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 12 types, 12 molecules MCFKGHILNRQO
#1: Protein | Mass: 27042.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SPT15 / Production host: ![]() ![]() |
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#3: Protein | Mass: 79995.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: GS115 / ATCC 20864 / Gene: PAS_chr1-4_0651 / Production host: ![]() ![]() |
#4: Protein | Mass: 59530.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QZ05 |
#8: Protein | Mass: 66690.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R150 |
#9: Protein | Mass: 80933.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R4L4 |
#10: Protein | Mass: 54888.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QW33 |
#11: Protein | Mass: 17303.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QZS5 |
#12: Protein | Mass: 438055.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QYV4 |
#14: Protein | Mass: 34059.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 8560.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#16: Protein | Mass: 56745.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QY61, ubiquitinyl hydrolase 1 |
#17: Protein | Mass: 13977.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R2D9 |
-Transcriptional ... , 2 types, 2 molecules AB
#2: Protein | Mass: 49888.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QZA3 |
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#13: Protein | Mass: 81864.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R2A4 |
-Subunit of the SAGA ... , 2 types, 2 molecules DE
#5: Protein | Mass: 39030.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R3E4 |
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#6: Protein | Mass: 136768.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R5C7 |
-Transcription ... , 2 types, 2 molecules JP
#7: Protein | Mass: 23879.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QXP2 |
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#18: Protein | Mass: 11126.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R1P1 |
-Non-polymers , 1 types, 91 molecules ![](data/chem/img/HOH.gif)
#19: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 1.6 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 4500 nm / Cs: 0.01 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 52.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1068534 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354104 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER |