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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 / TFIIA-class transcription factor complex binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III transcription regulatory region sequence-specific DNA binding / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of DNA-templated transcription, initiation ...SAGA-type complex / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / TFIIA-class transcription factor complex binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III transcription regulatory region sequence-specific DNA binding / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of DNA-templated transcription, initiation / transcription factor TFIIA complex / SAGA complex / transcription export complex 2 / RNA polymerase III general transcription initiation factor activity / RNA polymerase I general transcription initiation factor binding / histone H3-K79 methylation / RNA polymerase I preinitiation complex assembly / histone deubiquitination / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / go:0001302: / RNA polymerase II preinitiation complex assembly / hypothalamus gonadotrophin-releasing hormone neuron development / mitochondrion transport along microtubule / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / fat pad development / Ada2/Gcn5/Ada3 transcription activator complex / female meiosis I / poly(A)+ mRNA export from nucleus / histone H3-K4 methylation / positive regulation of protein monoubiquitination / DNA binding, bending / male meiosis I / female gonad development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / seminiferous tubule development / enzyme activator activity / regulation of neuron death / energy homeostasis / nuclear pore / histone acetyltransferase complex / transcription elongation from RNA polymerase II promoter / molecular adaptor activity / histone acetylation / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II activating transcription factor binding / histone acetyltransferase activity / MyD88-independent toll-like receptor signaling pathway / regulation of proteasomal protein catabolic process / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / positive regulation of protein ubiquitination / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / regulation of mitochondrial membrane potential / DNA-templated transcription, initiation / neuron projection morphogenesis / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / P-body / intracellular transport of virus / endosomal transport / nucleotide-excision repair, DNA incision, 5'-to lesion / regulation of protein localization / MyD88-dependent toll-like receptor signaling pathway / DNA damage response, detection of DNA damage / host cell / modification-dependent protein catabolic process / nucleotide-excision repair, DNA incision / protein targeting to peroxisome / error-free translesion synthesis / JNK cascade / transcription by RNA polymerase II / transcription coregulator activity / stress-activated MAPK cascade / protein tag / endocytic vesicle membrane / interstrand cross-link repair / error-prone translesion synthesis / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / I-kappaB kinase/NF-kappaB signaling / transcription-coupled nucleotide-excision repair / viral life cycle / negative regulation of transforming growth factor beta receptor signaling pathway / translesion synthesis / ubiquitinyl hydrolase 1 / transforming growth factor beta receptor signaling pathway / anaphase-promoting complex-dependent catabolic process / virion assembly / thiol-dependent ubiquitin-specific protease activity / regulation of mRNA stability / transmembrane transport / disordered domain specific binding / membrane organization / protein polyubiquitination / ubiquitin-dependent protein catabolic process / Wnt signaling pathway
Ubiquitin family / Ubiquitin domain / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / WD40-repeat-containing domain / Ubiquitin specific protease, conserved site / Bromodomain, conserved site / Transcription factor, enhancer of yellow 2 / Histone acetyltransferases subunit 3 / WD40 repeat, conserved site ...Ubiquitin family / Ubiquitin domain / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / WD40-repeat-containing domain / Ubiquitin specific protease, conserved site / Bromodomain, conserved site / Transcription factor, enhancer of yellow 2 / Histone acetyltransferases subunit 3 / WD40 repeat, conserved site / Ubiquitin conserved site / G-protein beta WD-40 repeat / SAGA complex, Sgf11 subunit / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Ubiquitin-like domain superfamily / TATA-box binding protein, conserved site / Transcription-associated protein 1 / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / Bromodomain-like superfamily / TFIID subunit TAF5, NTD2 domain superfamily / PIK-related kinase / SCA7 domain / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TAFII31 / Phosphatidylinositol 3-/4-kinase, catalytic domain / 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 IID, subunit 13 / Zinc finger, RING/FYVE/PHD-type / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TFIID, 23-30kDa subunit / TATA box binding protein associated factor (TAF) / LIS1 homology motif / TFIID subunit TAF5, NTD2 domain / Histone-fold / Protein kinase-like domain superfamily / TAF6, C-terminal HEAT repeat domain / TBP domain superfamily / Transcriptional activator Spt7 / Ubiquitin specific protease domain / Transcription factor e(y)2 / SCA7, zinc-binding domain / FAT domain / Transcription factor TFIID (or TATA-binding protein, TBP) / WD domain, G-beta repeat / Sgf11 (transcriptional regulation protein) / TATA box binding protein associated factor (TAF) / TAF6 C-terminal HEAT repeat domain / Spt20 family / Transcription initiation factor IID, 31kD subunit / Bromodomain / Transcription initiation factor IID, 18kD subunit / Ubiquitin carboxyl-terminal hydrolase / Zn-finger in ubiquitin-hydrolases and other protein / Transcription initiation factor TFIID 23-30kDa subunit / LisH / Histone acetyltransferases subunit 3 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 / Papain-like cysteine peptidase superfamily / Transcription factor EnY2 superfamily / Phosphatidylinositol 3- and 4-kinase / SAGA-associated factor 73 / Ubiquitin carboxyl-terminal hydrolase 8 / Transcription initiation factor TFIID subunit 6 / WD40 associated region in TFIID subunit, NTD2 domain
TATA-box-binding protein / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / Subunit (60 kDa) of TFIID and SAGA complexes / Transcription initiation factor TFIID subunit 10 / Ubiquitin carboxyl-terminal hydrolase / Transcription-associated protein / Uncharacterized protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes ...TATA-box-binding protein / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / Subunit (60 kDa) of TFIID and SAGA complexes / Transcription initiation factor TFIID subunit 10 / Ubiquitin carboxyl-terminal hydrolase / Transcription-associated protein / Uncharacterized protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Transcription and mRNA export factor SUS1 / SAGA-associated factor 11 / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / Subunit (90 kDa) of TFIID and SAGA complexes / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex / BJ4_G0016160.mRNA.1.CDS.1 / Polyubiquitin-B / Polyubiquitin-B / Subunit (61/68 kDa) of TFIID and SAGA complexes
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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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, UniProt: P13393*PLUS
#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, UniProt: P0CG47*PLUS
#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
IDNameTypeEntity IDParent-IDSource
1SAGA bound to TBPCOMPLEX#1-#180MULTIPLE SOURCES
2TATA-box binding protein (TBP)COMPLEX#11RECOMBINANT
3SAGA bound to TBPCOMPLEX#31RECOMBINANT
4SAGA bound to TBPCOMPLEX#151RECOMBINANT
5SAGACOMPLEX#2, #4-#14, #16-#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)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
14Escherichia coli (E. coli)562
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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