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- EMDB-10446: SAGA-TBP filtered to show the position of the DUB domain -

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Basic information

Entry
Database: EMDB / ID: EMD-10446
TitleSAGA-TBP filtered to show the position of the DUB domain
Map data
SampleSAGA bound to TBP
  • TATA-box binding protein (TBP)
  • SAGA
  • TATA-binding protein
  • (Transcriptional ...Transcription (biology)) x 2
  • Subunit of SAGA histone acetyltransferase complex
  • Spt20
  • (Subunit of the SAGA ...) x 2
  • (Transcription ...) x 2
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Transcription-associated protein
  • Spt8
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase
  • SAGA-associated factor 11
  • ligand
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 / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / 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 / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / 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 / transcription export complex 2 / SAGA complex / 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 / TRIF-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA duplex unwinding / 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 / protein targeting to peroxisome / nucleotide-excision repair, DNA incision / 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
Bromodomain / Transcription initiation factor TFIID, 23-30kDa subunit / Histone-fold / Transcription factor Spt20 / TFIID subunit TAF5, NTD2 domain / LIS1 homology motif / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain ...Bromodomain / Transcription initiation factor TFIID, 23-30kDa subunit / Histone-fold / Transcription factor Spt20 / TFIID subunit TAF5, NTD2 domain / LIS1 homology motif / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TAFII31 / FATC domain / Ubiquitin specific protease domain / Ubiquitin-like domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily / G-protein beta WD-40 repeat / TATA-box binding protein, eukaryotic / Bromodomain, conserved site / WD40/YVTN repeat-like-containing domain superfamily / PIK-related kinase / WD40-repeat-containing domain / Ubiquitin specific protease, conserved site / Zinc finger, UBP-type / SAGA complex, Sgf11 subunit / Transcription factor, enhancer of yellow 2 / Ubiquitin domain / Histone acetyltransferases subunit 3 / SCA7 domain / WD40 repeat, conserved site / Ubiquitin conserved site / Zinc finger, RING/FYVE/PHD-type / TBP domain superfamily / Transcription-associated protein 1 / TATA-box binding protein, conserved site / WD40-repeat-containing domain superfamily / Transcription initiation factor TFIID subunit 12 / TATA-box binding protein / Phosphatidylinositol 3-/4-kinase, catalytic domain / Transcription factor EnY2 superfamily / WD40 repeat / Papain-like cysteine peptidase superfamily / SAGA-associated factor 73 / Transcription initiation factor TFIID subunit 6 / Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin-like domain / PIK-related kinase, FAT / Transcriptional activator Spt7 / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Bromodomain-like superfamily / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TFIID subunit 5
Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Polyubiquitin-B / Polyubiquitin-B / BJ4_G0016160.mRNA.1.CDS.1 / 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 / Subunit (60 kDa) of TFIID and SAGA complexes / Transcription and mRNA export factor SUS1 ...Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Polyubiquitin-B / Polyubiquitin-B / BJ4_G0016160.mRNA.1.CDS.1 / 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 / Subunit (60 kDa) of TFIID and SAGA complexes / Transcription and mRNA export factor SUS1 / 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 / Subunit of SAGA histone acetyltransferase complex / Uncharacterized protein / Transcription-associated protein / Ubiquitin carboxyl-terminal hydrolase / Transcription initiation factor TFIID subunit 10 / TATA-box-binding protein
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Komagataella phaffii GS115 (fungus) / Homo sapiens (human) / Yeast (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsPapai G / Frechard A / Kolesnikova O / Crucifix C / Schultz P / Ben-Shem A
Funding support France, 3 items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-IDEX-0002-02 France
French National Research AgencyANR-10-LABX-0030-INRT 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 ReportSummary, Full report, XML, About validation report
History
DepositionNov 1, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tbm
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10446.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 256 pix.
= 558.08 Å
2.18 Å/pix.
x 256 pix.
= 558.08 Å
2.18 Å/pix.
x 256 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.023929587 - 0.031576734
Average (Standard dev.)0.0000095512 (±0.0011494906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0240.0320.000

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Supplemental data

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Sample components

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Entire SAGA bound to TBP

EntireName: SAGA bound to TBP / Number of components: 24

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Component #1: protein, SAGA bound to TBP

ProteinName: SAGA bound to TBP / Recombinant expression: No
MassExperimental: 1.6 MDa

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Component #2: protein, TATA-box binding protein (TBP)

ProteinName: TATA-box binding protein (TBP) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, SAGA bound to TBP

ProteinName: SAGA bound to TBP / Recombinant expression: No
SourceSpecies: Komagataella phaffii GS115 (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, SAGA bound to TBP

ProteinName: SAGA bound to TBP / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, SAGA

ProteinName: SAGA / Recombinant expression: No
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Component #6: protein, TATA-binding protein

ProteinName: TATA-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.042275 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Transcriptional coactivator HFI1/ADA1

ProteinName: Transcriptional coactivator HFI1/ADA1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.888273 kDa
SourceSpecies: Yeast (fungus)

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Component #8: protein, Subunit of SAGA histone acetyltransferase complex

ProteinName: Subunit of SAGA histone acetyltransferase complex / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.995227 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Spt20

ProteinName: Spt20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.530578 kDa
SourceSpecies: Yeast (fungus)

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Component #10: protein, Subunit of the SAGA and SAGA-like transcriptional regula...

ProteinName: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.030105 kDa
SourceSpecies: Yeast (fungus)

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Component #11: protein, Subunit of the SAGA transcriptional regulatory complex, ...

ProteinName: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 136.768828 kDa
SourceSpecies: Yeast (fungus)

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Component #12: protein, Transcription initiation factor TFIID subunit 10

ProteinName: Transcription initiation factor TFIID subunit 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.879145 kDa
SourceSpecies: Yeast (fungus)

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Component #13: protein, Subunit (61/68 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (61/68 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.690133 kDa
SourceSpecies: Yeast (fungus)

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Component #14: protein, Subunit (90 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (90 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.933008 kDa
SourceSpecies: Yeast (fungus)

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Component #15: protein, Subunit (60 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (60 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.888445 kDa
SourceSpecies: Yeast (fungus)

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Component #16: protein, Subunit (17 kDa) of TFIID and SAGA complexes, involved i...

ProteinName: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.303576 kDa
SourceSpecies: Yeast (fungus)

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Component #17: protein, Transcription-associated protein

ProteinName: Transcription-associated protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 438.055344 kDa
SourceSpecies: Yeast (fungus)

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Component #18: protein, Transcriptional regulator involved in glucose repression...

ProteinName: Transcriptional regulator involved in glucose repression of Gal4p-regulated genes
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.864305 kDa
SourceSpecies: Yeast (fungus)

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Component #19: protein, Spt8

ProteinName: Spt8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.059902 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

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Component #20: protein, Polyubiquitin-B

ProteinName: Polyubiquitin-B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.560831 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #21: protein, Ubiquitin carboxyl-terminal hydrolase

ProteinName: Ubiquitin carboxyl-terminal hydrolase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.745879 kDa
SourceSpecies: Yeast (fungus)

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Component #22: protein, SAGA-associated factor 11

ProteinName: SAGA-associated factor 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.977742 kDa
SourceSpecies: Yeast (fungus)

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Component #23: protein, Transcription and mRNA export factor SUS1

ProteinName: Transcription and mRNA export factor SUS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.126675 kDa
SourceSpecies: Yeast (fungus)

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Component #24: ligand, water

LigandName: water / Number of Copies: 91 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 52.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 354104
3D reconstructionSoftware: RELION / Resolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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