+Open data
-Basic information
Entry | Database: PDB / ID: 6tbm | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of SAGA bound to TBP, including Spt8 and DUB | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSCRIPTION / Transcriptional co-activator / Histone-acetylation | ||||||||||||
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 (fungus) Homo sapiens (human) Komagataella phaffii GS115 (fungus) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å | ||||||||||||
Authors | Papai, G. / Frechard, A. / Kolesnikova, O. / Crucifix, C. / Schultz, P. / Ben-Shem, A. | ||||||||||||
Funding support | France, 3items
| ||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tbm.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tbm.ent.gz | 940.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tbm ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tbm | HTTPS FTP |
---|
-Related structure data
Related structure data | 10446MC 6tb4C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Gene: SPT15 / Production host: Escherichia coli (E. coli) / References: UniProt: P13393*PLUS |
---|---|
#3: Protein | Mass: 79995.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / Gene: PAS_chr1-4_0651 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ39 |
#4: Protein | Mass: 59530.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 |
#15: Protein | Mass: 8560.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39, UniProt: P0CG47*PLUS |
#16: Protein | Mass: 56745.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4QZA3 |
---|---|
#13: Protein | Mass: 81864.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R3E4 |
---|---|
#6: Protein | Mass: 136768.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) 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) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4QXP2 |
---|---|
#18: Protein | Mass: 11126.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R1P1 |
-Non-polymers , 1 types, 91 molecules
#19: Water | ChemComp-HOH / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.6 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||||||||
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |