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- EMDB-10416: nucleosome-bound state of SAGA coactivator -

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Basic information

Entry
Database: EMDB / ID: EMD-10416
Titlenucleosome-bound state of SAGA coactivator
Map datanucleosome-bound state of SAGA
Sample
  • Complex: SAGA coactivator
Function / homology
Function and homology information


RITS complex assembly / conjugation with cellular fusion / DUBm complex / pseudohyphal growth / : / : / positive regulation of DNA-templated transcription initiation / : / invasive growth in response to glucose limitation / regulation of nucleocytoplasmic transport ...RITS complex assembly / conjugation with cellular fusion / DUBm complex / pseudohyphal growth / : / : / positive regulation of DNA-templated transcription initiation / : / invasive growth in response to glucose limitation / regulation of nucleocytoplasmic transport / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / NuA4 histone acetyltransferase complex / RNA polymerase II transcribes snRNA genes / 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 / RNA Polymerase II Pre-transcription Events / IRE1-mediated unfolded protein response / enzyme activator activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / ubiquitin binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / chromatin organization / protein-containing complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / molecular adaptor activity / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin binding / structural molecule activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcriptional activator Spt7 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73, zinc finger domain / Zinc finger domain / SAGA-associated factor 73 / SCA7 domain ...Transcriptional activator Spt7 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73, zinc finger domain / Zinc finger domain / SAGA-associated factor 73 / SCA7 domain / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / SCA7, zinc-binding domain / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / SCA7 domain profile. / LisH / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein SPT3 / Transcriptional activator SPT7 / Transcription initiation factor TFIID subunit 5 / Transcription-associated protein 1 / Transcription factor SPT20 / Transcription initiation factor TFIID subunit 6 / SAGA-associated factor 73 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 10 / Transcriptional coactivator HFI1/ADA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsWang H / Cramer P
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationSFB860, SPP1935, EXC 2067/1-390729940 Germany
European Research Council693023 Germany
CitationJournal: Nature / Year: 2020
Title: Structure of the transcription coactivator SAGA.
Authors: Haibo Wang / Christian Dienemann / Alexandra Stützer / Henning Urlaub / Alan C M Cheung / Patrick Cramer /
Abstract: Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) and transcription factor IID (TFIID). SAGA is ...Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) and transcription factor IID (TFIID). SAGA is required for all regulated transcription and is conserved among eukaryotes. SAGA contains four modules: the activator-binding Tra1 module, the core module, the histone acetyltransferase (HAT) module and the histone deubiquitination (DUB) module. Previous studies provided partial structures, but the structure of the central core module is unknown. Here we present the cryo-electron microscopy structure of SAGA from the yeast Saccharomyces cerevisiae and resolve the core module at 3.3 Å resolution. The core module consists of subunits Taf5, Sgf73 and Spt20, and a histone octamer-like fold. The octamer-like fold comprises the heterodimers Taf6-Taf9, Taf10-Spt7 and Taf12-Ada1, and two histone-fold domains in Spt3. Spt3 and the adjacent subunit Spt8 interact with the TATA box-binding protein (TBP). The octamer-like fold and its TBP-interacting region are similar in TFIID, whereas Taf5 and the Taf6 HEAT domain adopt distinct conformations. Taf12 and Spt20 form flexible connections to the Tra1 module, whereas Sgf73 tethers the DUB module. Binding of a nucleosome to SAGA displaces the HAT and DUB modules from the core-module surface, allowing the DUB module to bind one face of an ubiquitinated nucleosome.
History
DepositionOct 28, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseJan 29, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10416.png

Downloads & links

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Map

FileDownload / File: emd_10416.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnucleosome-bound state of SAGA
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.010986022 - 0.0573136
Average (Standard dev.)8.205765e-05 (±0.0017569861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 548.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z548.000548.000548.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0110.0570.000

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Supplemental data

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Additional map: Focus-refined map

Fileemd_10416_additional.map
AnnotationFocus-refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map

Fileemd_10416_additional_1.map
AnnotationFocus-refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SAGA coactivator

EntireName: SAGA coactivator
Components
  • Complex: SAGA coactivator

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Supramolecule #1: SAGA coactivator

SupramoleculeName: SAGA coactivator / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 450 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClSodium chloridesodium chloride
1.0 mMC4H10O2S2Dithiothreitol

Details: Solution were made from stock solution
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 44.17 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 250368
CTF correctionSoftware - Name: Warp (ver. 1.0.6)
Startup modelType of model: INSILICO MODEL
In silico model: cryoSPARC ab-initio reconstruction was use to generate the startup model.
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.5)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 86910
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 107.1 / Target criteria: Correlation coefficient

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