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- PDB-6tbm: Structure of SAGA bound to TBP, including Spt8 and DUB -

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Database: PDB / ID: 6tbm
TitleStructure of SAGA bound to TBP, including Spt8 and DUB
Components
  • (Subunit of the SAGA ...) x 2
  • (Transcription ...) x 2
  • (Transcriptional ...Transcription (biology)) x 2
  • Polyubiquitin-B
  • SAGA-associated factor 11
  • Spt20
  • Spt8
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • Subunit of SAGA histone acetyltransferase complex
  • TATA-binding protein
  • Transcription-associated protein
  • Ubiquitin carboxyl-terminal hydrolase
KeywordsTRANSCRIPTION / Transcriptional co-activator / Histone-acetylation
Function / homology
Function and homology information


SAGA-type complex / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SAGA complex / transcription export complex 2 / histone H3-K79 methylation / histone deubiquitination / poly(A)+ mRNA export from nucleus ...SAGA-type complex / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SAGA complex / transcription export complex 2 / histone H3-K79 methylation / histone deubiquitination / poly(A)+ mRNA export from nucleus / Ada2/Gcn5/Ada3 transcription activator complex / histone H3-K4 methylation / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / molecular adaptor activity / histone acetyltransferase complex / transcription coregulator activity / histone acetylation / transcription elongation from RNA polymerase II promoter / thiol-dependent ubiquitin-specific protease activity / nuclear pore / histone acetyltransferase activity / ubiquitinyl hydrolase 1 / RNA polymerase II activating transcription factor binding / DNA-templated transcription, initiation / enzyme activator activity / regulation of protein localization / P-body / transcription by RNA polymerase II / transferase activity / ubiquitin-dependent protein catabolic process / transcription coactivator activity / regulation of transcription by RNA polymerase II / chromatin binding / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / identical protein binding / nucleus / cytosol
LIS1 homology motif / Histone-fold / Ubiquitin-like domain / TATA-box binding protein / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Bromodomain / Zinc finger, UBP-type / WD40 repeat / PIK-related kinase, FAT / FATC domain ...LIS1 homology motif / Histone-fold / Ubiquitin-like domain / TATA-box binding protein / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Bromodomain / Zinc finger, UBP-type / WD40 repeat / PIK-related kinase, FAT / FATC domain / Transcription initiation factor TAFII31 / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TFIID, 23-30kDa subunit / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Protein kinase-like domain superfamily / G-protein beta WD-40 repeat / WD40-repeat-containing domain / Ubiquitin conserved site / WD40 repeat, conserved site / Histone acetyltransferases subunit 3 / Transcription factor, enhancer of yellow 2 / Bromodomain, conserved site / Ubiquitin specific protease, conserved site / Armadillo-type fold / TAF6, C-terminal HEAT repeat domain / WD40/YVTN repeat-like-containing domain superfamily / PIK-related kinase / SAGA complex, Sgf11 subunit / SCA7 domain / Zinc finger, RING/FYVE/PHD-type / TBP domain superfamily / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ubiquitin domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / Bromodomain-like superfamily / Transcription factor EnY2 superfamily / WD40-repeat-containing domain superfamily / TATA-box binding protein, eukaryotic / Transcription-associated protein 1 / Papain-like cysteine peptidase superfamily / Transcription initiation factor TFIID subunit 6 / TATA-box binding protein, conserved site / SAGA-associated factor 73 / Ubiquitin-like domain superfamily / Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin specific protease domain / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcription factor Spt20 / Transcriptional activator Spt7
Transcription and mRNA export factor SUS1 / TATA-binding protein / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex / Subunit (90 kDa) of TFIID and SAGA complexes / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / SAGA-associated factor 11 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Subunit of SAGA histone acetyltransferase complex / Subunit (61/68 kDa) of TFIID and SAGA complexes / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation ...Transcription and mRNA export factor SUS1 / TATA-binding protein / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex / Subunit (90 kDa) of TFIID and SAGA complexes / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / SAGA-associated factor 11 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Subunit of SAGA histone acetyltransferase complex / Subunit (61/68 kDa) of TFIID and SAGA complexes / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / Transcriptional coactivator HFI1/ADA1 / Uncharacterized protein / Transcription-associated protein / Ubiquitin carboxyl-terminal hydrolase / Transcription initiation factor TFIID subunit 10 / Subunit (60 kDa) of TFIID and SAGA complexes / Polyubiquitin-B
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Komagataella phaffii (fungus)
Homo sapiens (human)
Komagataella phaffii GS115 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsPapai, G. / Frechard, A. / Kolesnikova, O. / Crucifix, C. / Schultz, P. / Ben-Shem, A.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
M: TATA-binding protein
A: Transcriptional coactivator HFI1/ADA1
C: Subunit of SAGA histone acetyltransferase complex
F: Spt20
D: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
E: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
J: Transcription initiation factor TFIID subunit 10
K: Subunit (61/68 kDa) of TFIID and SAGA complexes
G: Subunit (90 kDa) of TFIID and SAGA complexes
H: Subunit (60 kDa) of TFIID and SAGA complexes
I: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
L: Transcription-associated protein
B: Transcriptional regulator involved in glucose repression of Gal4p-regulated genes
N: Spt8
R: Polyubiquitin-B
Q: Ubiquitin carboxyl-terminal hydrolase
O: SAGA-associated factor 11
P: Transcription and mRNA export factor SUS1


Theoretical massNumber of molelcules
Total (without water)1,280,34018
Polymers1,280,34018
Non-polymers00
Water1,63991
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 12 types, 12 molecules MCFKGHILNRQO

#1: Protein TATA-binding protein /


Mass: 27042.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SPT15 / Production host: Escherichia coli (E. coli) / References: UniProt: G4XSG8
#3: Protein Subunit of SAGA histone acetyltransferase complex


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)
Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ39
#4: Protein Spt20


Mass: 59530.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QZ05
#8: Protein Subunit (61/68 kDa) of TFIID and SAGA complexes


Mass: 66690.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R150
#9: Protein Subunit (90 kDa) of TFIID and SAGA complexes


Mass: 80933.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R4L4
#10: Protein Subunit (60 kDa) of TFIID and SAGA complexes


Mass: 54888.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QW33
#11: Protein Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation


Mass: 17303.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QZS5
#12: Protein Transcription-associated 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)
References: UniProt: C4QYV4
#14: Protein Spt8


Mass: 34059.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus)
#15: Protein Polyubiquitin-B


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
#16: Protein Ubiquitin carboxyl-terminal hydrolase


Mass: 56745.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QY61, ubiquitinyl hydrolase 1
#17: Protein SAGA-associated factor 11


Mass: 13977.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R2D9

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Transcriptional ... , 2 types, 2 molecules AB

#2: Protein Transcriptional coactivator HFI1/ADA1


Mass: 49888.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QZA3
#13: Protein Transcriptional regulator involved in glucose repression of Gal4p-regulated genes


Mass: 81864.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R2A4

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Subunit of the SAGA ... , 2 types, 2 molecules DE

#5: Protein Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act


Mass: 39030.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R3E4
#6: Protein Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex


Mass: 136768.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R5C7

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Transcription ... , 2 types, 2 molecules JP

#7: Protein Transcription initiation factor TFIID subunit 10


Mass: 23879.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QXP2
#18: Protein Transcription and mRNA export factor SUS1


Mass: 11126.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R1P1

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Non-polymers , 1 types, 91 molecules

#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1SAGA bound to TBP1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,180MULTIPLE SOURCES
2TATA-box binding protein (TBP)11RECOMBINANT
3SAGA bound to TBP31RECOMBINANT
4SAGA bound to TBP151RECOMBINANT
5SAGA2,4,5,6,7,8,9,10,11,12,13,14,16,17,181NATURAL
Molecular weightValue: 1.6 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (baker's yeast)4932
23Komagataella phaffii GS115 (fungus)644223
34Homo sapiens (human)9606
45Komagataella phaffii GS115 (fungus)644223
Source (recombinant)

Ncbi tax-ID: 562 / Organism: Escherichia coli (E. coli)

IDEntity assembly-ID
12
23
14
Buffer solutionpH: 8
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEM3.8 betaimage acquisition
4WarpCTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1068534
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354104 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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