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- EMDB-10413: SAGA Tra1 module -

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Basic information

Entry
Database: EMDB / ID: EMD-10413
TitleSAGA Tra1 module
Map datalocal resolution filtered map
Sample
  • Complex: SAGA Tra1 module
    • Protein or peptide: Transcription factor SPT20
    • Protein or peptide: Transcription initiation factor TFIID subunit 12
    • Protein or peptide: Transcription-associated protein 1
KeywordsCoactivator / Transcription / Histone acetyltransferase / Histone deubiquitinase / GENE REGULATION
Function / homology
Function and homology information


SLIK (SAGA-like) complex / SAGA complex / 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 / RNA Polymerase II Pre-transcription Events / NuA4 histone acetyltransferase complex / IRE1-mediated unfolded protein response / transcription factor TFIID complex ...SLIK (SAGA-like) complex / SAGA complex / 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 / RNA Polymerase II Pre-transcription Events / NuA4 histone acetyltransferase complex / IRE1-mediated unfolded protein response / transcription factor TFIID complex / Ub-specific processing proteases / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription coregulator activity / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / molecular adaptor activity / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 domain ...Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 domain / 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 / Histone-fold / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transcription-associated protein 1 / Transcription factor SPT20 / Transcription initiation factor TFIID subunit 12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang H / Cheung A
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 6, 2019-
Map releaseJan 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t9j
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10413.png

Downloads & links

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Map

FileDownload / File: emd_10413.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.26651654 - 0.5487442
Average (Standard dev.)0.0006686602 (±0.008874099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2670.5490.001

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Supplemental data

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Half map: half map 1

Fileemd_10413_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_10413_half_map_2.map
Annotationhalf map 2
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 Tra1 module

EntireName: SAGA Tra1 module
Components
  • Complex: SAGA Tra1 module
    • Protein or peptide: Transcription factor SPT20
    • Protein or peptide: Transcription initiation factor TFIID subunit 12
    • Protein or peptide: Transcription-associated protein 1

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Supramolecule #1: SAGA Tra1 module

SupramoleculeName: SAGA Tra1 module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Transcription factor SPT20

MacromoleculeName: Transcription factor SPT20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 67.880312 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSANSPTGND PHVFGIPVNA TPSNMGSPGS PVNVPPPMNP AVANVNHPVM RTNSNSNANE GTRTLTREQI QQLQQRQRLL LQQRLLEQQ RKQQALQNYE AQFYQMLMTL NKRPKRLYNF VEDADSILKK YEQYLHSFEF HIYENNYKIC APANSRLQQQ Q KQPELTSD ...String:
MSANSPTGND PHVFGIPVNA TPSNMGSPGS PVNVPPPMNP AVANVNHPVM RTNSNSNANE GTRTLTREQI QQLQQRQRLL LQQRLLEQQ RKQQALQNYE AQFYQMLMTL NKRPKRLYNF VEDADSILKK YEQYLHSFEF HIYENNYKIC APANSRLQQQ Q KQPELTSD GLILTKNNET LKEFLEYVAR GRIPDAIMEV LRDCNIQFYE GNLILQVYDH TNTVDVTPKE NKPNLNSSSS PS NNNSTQD NSKIQQPSEP NSGVANTGAN TANKKASFKR PRVYRTLLKP NDLTTYYDMM SYADNARFSD SIYQQFESEI LTL TKRNLS LSVPLNPYEH RDMLEETAFS EPHWDSEKKS FIHEHRAEST REGTKGVVGH IEERDEFPQH SSNYEQLMLI MNER TTTIT NSTFAVSLTK NAMEIASSSS NGVRGASSST SNSASNTRNN SLANGNQVAL AAAAAAAAVG STMGNDNNQF SRLKF IEQW RINKEKRKQQ ALSANINPTP FNARISMTAP LTPQQQLLQR QQQALEQQQN GGAMKNANKR SGNNATSNNN NNNNNL DKP KVKRPRKNAK KSESGTPAPK KKRMTKKKQS ASSTPSSTTM S

UniProtKB: Transcription factor SPT20

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Macromolecule #2: Transcription initiation factor TFIID subunit 12

MacromoleculeName: Transcription initiation factor TFIID subunit 12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 61.144379 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSSNPENSGV NANNNTGTGN ADAITGAQQN MVLQPRQLQE MAAKFRTLLT EARNVGETTP RGKELMFQAA KIKQVYDALT LNRRRQQAA QAYNNTSNSN SSNPASIPTE NVPNSSQQQQ QQQQQTRNNS NKFSNMIKQV LTPEENQEYE KLWQNFQVRH T SIKEKETY ...String:
MSSNPENSGV NANNNTGTGN ADAITGAQQN MVLQPRQLQE MAAKFRTLLT EARNVGETTP RGKELMFQAA KIKQVYDALT LNRRRQQAA QAYNNTSNSN SSNPASIPTE NVPNSSQQQQ QQQQQTRNNS NKFSNMIKQV LTPEENQEYE KLWQNFQVRH T SIKEKETY LKQNIDRLEQ EINKQTDEGP KQQLQEKKIE LLNDWKVLKI EYTKLFNNYQ NSKKTFYVEC ARHNPALHKF LQ ESTQQQR VQQQRVQQQQ QQQQQQQQQQ QQQQQQQQQR QGQNQRKISS SNSTEIPSVT GPDALKSQQQ QQNTITATNN PRG NVNTSQ TEQSKAKVTN VNATASMLNN ISSSKSAIFK QTEPAIPISE NISTKTPAPV AYRSNRPTIT GGSAMNASAL NTPA TTKLP PYEMDTQRVM SKRKLRELVK TVGIDEGDGE TVIDGDVEEL LLDLADDFVT NVTAFSCRLA KHRKSDNLEA RDIQL HLER NWNIRIPGYS ADEIRSTRKW NPSQNYNQKL QSITSDKVAA AKNNGNNVAS LNTKK

UniProtKB: Transcription initiation factor TFIID subunit 12

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Macromolecule #3: Transcription-associated protein 1

MacromoleculeName: Transcription-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 433.677281 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG ...String:
MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG DLDSPKEPQA DELLDEFSKN DEEKDFPSKQ SSTEPRFENS TSSNGLRSSM FSFKILSECP ITMVTLYSSY KQ LTSTSLP EFTPLIMNLL NIQIKQQQEA REQAESRGEH FTSISTEIIN RPAYCDFILA QIKATSFLAY VFIRGYAPEF LQD YVNFVP DLIIRLLQDC PSELSSARKE LLHATRHILS TNYKKLFLPK LDYLFDERIL IGNGFTMHET LRPLAYSTVA DFIH NIRSE LQLSEIEKTI KIYTGYLLDE SLALTVQIMS AKLLLNLVER ILKLGKENPQ EAPRAKKLLM IIIDSYMNRF KTLNR QYDT IMKYYGRYET HKKEKAEKLK NSIQDNDKES EEFMRKVLEP SDDDHLMPQP KKEDINDSPD VEMTESDKVV KNDVEM FDI KNYAPILLLP TPTNDPIKDA FYLYRTLMSF LKTIIHDLKV FNPPPNEYTV ANPKLWASVS RVFSYEEVIV FKDLFHE CI IGLKFFKDHN EKLSPETTKK HFDISMPSLP VSATKDAREL MDYLAFMFMQ MDNATFNEII EQELPFVYER MLEDSGLL H VAQSFLTSEI TSPNFAGILL RFLKGKLKDL GNVDFNTSNV LIRLFKLSFM SVNLFPNINE VVLLPHLNDL ILNSLKYST TAEEPLVYFY LIRTLFRSIG GGRFENLYRS IKPILQVLLQ SLNQMILTAR LPHERELYVE LCITVPVRLS VLAPYLPFLM KPLVFALQQ YPDLVSQGLR TLELCIDNLT AEYFDPIIEP VIDDVSKALF NLLQPQPFNH AISHNVVRIL GKLGGRNRQF L KPPTDLTE KTELDIDAIA DFKINGMPED VPLSVTPGIQ SALNILQSYK SDIHYRKSAY KYLTCVLLLM TKSSAEFPTN YT ELLKTAV NSIKLERIGI EKNFDLEPTV NKRDYSNQEN LFLRLLESVF YATSIKELKD DAMDLLNNLL DHFCLLQVNT TLL NKRNYN GTFNIDLKNP NFMLDSSLIL DAIPFALSYY IPEVREVGVL AYKRIYEKSC LIYGEELALS HSFIPELAKQ FIHL CYDET YYNKRGGVLG IKVLIDNVKS SSVFLKKYQY NLANGLLFVL KDTQSEAPSA ITDSAEKLLI DLLSITFADV KEEDL GNKV LENTLTDIVC ELSNANPKVR NACQKSLHTI SNLTGIPIVK LMDHSKQFLL SPIFAKPLRA LPFTMQIGNV DAITFC LSL PNTFLTFNEE LFRLLQESIV LADAEDESLS TNIQKTTEYS TSEQLVQLRI ACIKLLAIAL KNEEFATAQQ GNIRIRI LA VFFKTMLKTS PEIINTTYEA LKGSLAENSK LPKELLQNGL KPLLMNLSDH QKLTVPGLDA LSKLLELLIA YFKVEIGR K LLDHLTAWCR VEVLDTLFGQ DLAEQMPTKI IVSIINIFHL LPPQADMFLN DLLLKVMLLE RKLRLQLDSP FRTPLARYL NRFHNPVTEY FKKNMTLRQL VLFMCNIVQR PEAKELAEDF EKELDNFYDF YISNIPKNQV RVVSFFTNMV DLFNTMVITN GDEWLKKKG NMILKLKDML NLTLKTIKEN SFYIDHLQLN QSIAKFQALY LRFTELSERD QNPLLLDFID FSFSNGIKAS Y SLKKFIFH NIIASSNKEK QNNFINDATL FVLSDKCLDA RIFVLKNVIN STLIYEVATS GSLKSYLVED KKPKWLELLH NK IWKNSNA ILAYDVLDHH DLFRFELLQL SAIFIKADPE IIAEIKKDII KFCWNFIKLE DTLIKQSAYL VTSYFISKFD FPI KVVTQV FVALLRSSHV EARYLVKQSL DVLTPVLHER MNAAGTPDTW INWVKRVMVE NSSSQNNILY QFLISHPDLF FNSR DLFIS NIIHHMNKIT FMSNSNSDSH TLAIDLASLI LYWENKTLEI TNVNNTKTDS DGDVVMSDSK SDINPVEADT TAIIV DANN NSPISLHLRE ACTAFLIRYV CASNHRAIET ELGLRAINIL SELISDKHWT NVNVKLVYFE KFLIFQDLDS ENILYY CMN ALDVLYVFFK NKTKEWIMEN LPTIQNLLEK CIKSDHHDVQ EALQKVLQVI MKAIKAQGVS VIIEEESPGK TFIQMLT SV ITQDLQETSS VTAGVTLAWV LFMNFPDNIV PLLTPLMKTF SKLCKDHLSI SQPKDAMALE EARITTKLLE KVLYILSL K VSLLGDSRRP FLSTVALLID HSMDQNFLRK IVNMSRSWIF NTEIFPTVKE KAAILTKMLA FEIRGEPSLS KLFYEIVLK LFDQEHFNNT EITVRMEQPF LVGTRVEDIG IRKRFMTILD NSLERDIKER LYYVIRDQNW EFIADYPWLN QALQLLYGSF NREKELSLK NIYCLSPPSI LQEYLPENAE MVTEVNDLEL SNFVKGHIAS MQGLCRIISS DFIDSLIEIF YQDPKAIHRA W VTLFPQVY KSIPKNEKYG FVRSIITLLS KPYHTRQISS RTNVINMLLD SISKIESLEL PPHLVKYLAI SYNAWYQSIN IL ESIQSNT SIDNTKIIEA NEDALLELYV NLQEEDMFYG LWRRRAKYTE TNIGLSYEQI GLWDKAQQLY EVAQVKARSG ALP YSQSEY ALWEDNWIQC AEKLQHWDVL TELAKHEGFT DLLLECGWRV ADWNSDRDAL EQSVKSVMDV PTPRRQMFKT FLAL QNFAE SRKGDQEVRK LCDEGIQLSL IKWVSLPIRY TPAHKWLLHG FQQYMEFLEA TQIYANLHTT TVQNLDSKAQ EIKRI LQAW RDRLPNTWDD VNMWNDLVTW RQHAFQVINN AYLPLIPALQ QSNSNSNINT HAYRGYHEIA WVINRFAHVA RKHNMP DVC ISQLARIYTL PNIEIQEAFL KLREQAKCHY QNMNELTTGL DVISNTNLVY FGTVQKAEFF TLKGMFLSKL RAYEEAN QA FATAVQIDLN LAKAWAQWGF FNDRRLSEEP NNISFASNAI SCYLQAAGLY KNSKIRELLC RILWLISIDD ASGMLTNA F DSFRGEIPVW YWITFIPQLL TSLSHKEANM VRHILIRIAK SYPQALHFQL RTTKEDFAVI QRQTMAVMGD KPDTNDRNG RRQPWEYLQE LNNILKTAYP LLALSLESLV AQINDRFKST TDEDLFRLIN VLLIDGTLNY NRLPFPRKNP KLPENTEKNL VKFSTTLLA PYIRPKFNAD FIDNKPDYET YIKRLRYWRR RLENKLDRAS KKENLEVLCP HLSNFHHQKF EDIEIPGQYL L NKDNNVHF IKIARFLPTV DFVRGTHSSY RRLMIRGHDG SVHSFAVQYP AVRHSRREER MFQLYRLFNK SLSKNVETRR RS IQFNLPI AIPLSPQVRI MNDSVSFTTL HEIHNEFCKK KGFDPDDIQD FMADKLNAAH DDALPAPDMT ILKVEIFNSI QTM FVPSNV LKDHFTSLFT QFEDFWLFRK QFASQYSSFV FMSYMMMINN RTPHKIHVDK TSGNVFTLEM LPSRFPYERV KPLL KNHDL SLPPDSPIFH NNEPVPFRLT PNIQSLIGDS ALEGIFAVNL FTISRALIEP DNELNTYLAL FIRDEIISWF SNLHR PIIE NPQLREMVQT NVDLIIRKVA QLGHLNSTPT VTTQFILDCI GSAVSPRNLA RTDVNFMPWF

UniProtKB: Transcription-associated protein 1

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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 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 42.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 250368
Startup modelType of model: INSILICO MODEL
In silico model: cryoSPARC ab-initio reconstruction was use to generate the startup model.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 27602
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 107.1 / Target criteria: Correlation coefficient
Output model

PDB-6t9j:
SAGA Tra1 module

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