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- EMDB-10414: SAGA Core module -

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Basic information

Entry
Database: EMDB / ID: EMD-10414
TitleSAGA Core module
Map datalocal resolution filtered map
Sample
  • Complex: SAGA Core module
    • Protein or peptide: x 11 types
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 / 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 / chromatin binding / regulation of transcription by RNA polymerase II / structural molecule activity / 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 / SCA7, zinc-binding domain / 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 / 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
Similarity search - Domain/homology
Protein SPT3 / Transcriptional activator SPT7 / Transcription initiation factor TFIID subunit 5 / 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) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang H / Cheung A / 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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing 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-6t9k
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10414.png

Downloads & links

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Map

FileDownload / File: emd_10414.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-0.35927883 - 0.537432
Average (Standard dev.)0.0006481945 (±0.007770653)
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-0.3590.5370.001

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Supplemental data

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Half map: #1

Fileemd_10414_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10414_half_map_2.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 Core module

EntireName: SAGA Core module
Components
  • Complex: SAGA Core module
    • Protein or peptide: Transcription factor SPT20SPT20
    • Protein or peptide: Protein SPT3
    • Protein or peptide: Transcription initiation factor TFIID subunit 5
    • Protein or peptide: Transcription initiation factor TFIID subunit 6
    • Protein or peptide: Transcription initiation factor TFIID subunit 9
    • Protein or peptide: Transcription initiation factor TFIID subunit 10
    • Protein or peptide: Transcriptional coactivator HFI1/ADA1
    • Protein or peptide: Transcription initiation factor TFIID subunit 12
    • Protein or peptide: Transcriptional activator SPT7
    • Protein or peptide: SAGA-associated factor 73
    • Protein or peptide: unassigned sequence

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Supramolecule #1: SAGA Core module

SupramoleculeName: SAGA Core module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 500 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: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 67.880312 KDa
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

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Macromolecule #2: Protein SPT3

MacromoleculeName: Protein SPT3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 38.864082 KDa
SequenceString: MMDKHKYRVE IQQMMFVSGE INDPPVETTS LIEDIVRGQV IEILLQSNKT AHLRGSRSIL PEDVIFLIRH DKAKVNRLRT YLSWKDLRK NAKDQDASAG VASGTGNPGA GGEDDLKKAG GGEKDEKDGG NMMKVKKSQI KLPWELQFMF NEHPLENNDD N DDMDEDER ...String:
MMDKHKYRVE IQQMMFVSGE INDPPVETTS LIEDIVRGQV IEILLQSNKT AHLRGSRSIL PEDVIFLIRH DKAKVNRLRT YLSWKDLRK NAKDQDASAG VASGTGNPGA GGEDDLKKAG GGEKDEKDGG NMMKVKKSQI KLPWELQFMF NEHPLENNDD N DDMDEDER EANIVTLKRL KMADDRTRNM TKEEYVHWSD CRQASFTFRK NKRFKDWSGI SQLTEGKPHD DVIDILGFLT FE IVCSLTE TALKIKQREQ VLQTQKDKSQ QSSQDNTNFE FASSTLHRKK RLFDGPENVI NPLKPRHIEE AWRVLQTIDM RHR ALTNFK GGRLSSKPII M

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Macromolecule #3: Transcription initiation factor TFIID subunit 5

MacromoleculeName: Transcription initiation factor TFIID subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 89.081539 KDa
SequenceString: MSQKQSTNQN QNGTHQPQPV KNQRTNNAAG ANSGQQPQQQ SQGQSQQQGR SNGPFSASDL NRIVLEYLNK KGYHRTEAML RAESGRTLT PQNKQSPANT KTGKFPEQSS IPPNPGKTAK PISNPTNLSS KRDAEGGIVS SGRLEGLNAP ENYIRAYSML K NWVDSSLE ...String:
MSQKQSTNQN QNGTHQPQPV KNQRTNNAAG ANSGQQPQQQ SQGQSQQQGR SNGPFSASDL NRIVLEYLNK KGYHRTEAML RAESGRTLT PQNKQSPANT KTGKFPEQSS IPPNPGKTAK PISNPTNLSS KRDAEGGIVS SGRLEGLNAP ENYIRAYSML K NWVDSSLE IYKPELSYIM YPIFIYLFLN LVAKNPVYAR RFFDRFSPDF KDFHGSEINR LFSVNSIDHI KENEVASAFQ SH KYRITMS KTTLNLLLYF LNENESIGGS LIISVINQHL DPNIVESVTA REKLADGIKV LSDSENGNGK QNLEMNSVPV KLG PFPKDE EFVKEIETEL KIKDDQEKQL NQQTAGDNYS GANNRTLLQE YKAMNNEKFK DNTGDDDKDK IKDKIAKDEE KKES ELKVD GEKKDSNLSS PARDILPLPP KTALDLKLEI QKVKESRDAI KLDNLQLALP SVCMYTFQNT NKDMSCLDFS DDCRI AAAG FQDSYIKIWS LDGSSLNNPN IALNNNDKDE DPTCKTLVGH SGTVYSTSFS PDNKYLLSGS EDKTVRLWSM DTHTAL VSY KGHNHPVWDV SFSPLGHYFA TASHDQTARL WSCDHIYPLR IFAGHLNDVD CVSFHPNGCY VFTGSSDKTC RMWDVST GD SVRLFLGHTA PVISIAVCPD GRWLSTGSED GIINVWDIGT GKRLKQMRGH GKNAIYSLSY SKEGNVLISG GADHTVRV W DLKKATTEPS AEPDEPFIGY LGDVTASINQ DIKEYGRRRT VIPTSDLVAS FYTKKTPVFK VKFSRSNLAL AGGAFRP

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Macromolecule #4: Transcription initiation factor TFIID subunit 6

MacromoleculeName: Transcription initiation factor TFIID subunit 6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.964633 KDa
SequenceString: MSTQQQSYTI WSPQDTVKDV AESLGLENIN DDVLKALAMD VEYRILEIIE QAVKFKRHSK RDVLTTDDVS KALRVLNVEP LYGYYDGSE VNKAVSFSKV NTSGGQSVYY LDEEEVDFDR LINEPLPQVP RLPTFTTHWL AVEGVQPAII QNPNLNDIRV S QPPFIRGA ...String:
MSTQQQSYTI WSPQDTVKDV AESLGLENIN DDVLKALAMD VEYRILEIIE QAVKFKRHSK RDVLTTDDVS KALRVLNVEP LYGYYDGSE VNKAVSFSKV NTSGGQSVYY LDEEEVDFDR LINEPLPQVP RLPTFTTHWL AVEGVQPAII QNPNLNDIRV S QPPFIRGA IVTALNDNSL QTPVTSTTAS ASVTDTGASQ HLSNVKPGQN TEVKPLVKHV LSKELQIYFN KVISTLTAKS QA DEAAQHM KQAALTSLRT DSGLHQLVPY FIQFIAEQIT QNLSDLQLLT TILEMIYSLL SNTSIFLDPY IHSLMPSILT LLL AKKLGG SPKDDSPQEI HEFLERTNAL RDFAASLLDY VLKKFPQAYK SLKPRVTRTL LKTFLDINRV FGTYYGCLKG VSVL EGESI RFFLGNLNNW ARLVFNESGI TLDNIEEHLN DDSNPTRTKF TKEETQILVD TVISALLVLK KDLPDLYEGK GEKVT DEDK EKLLERCGVT IGFHILKRDD AKELISAIFF GE

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Macromolecule #5: Transcription initiation factor TFIID subunit 9

MacromoleculeName: Transcription initiation factor TFIID subunit 9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.334615 KDa
SequenceString:
MNGGGKNVLN KNSVGSVSEV GPDSTQEETP RDVRLLHLLL ASQSIHQYED QVPLQLMDFA HRYTQGVLKD ALVYNDYAGS GNSAGSGLG VEDIRLAIAA RTQYQFKPTA PKELMLQLAA ERNKKALPQV MGTWGVRLPP EKYCLTAKEW DLEDPKSM

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Macromolecule #6: Transcription initiation factor TFIID subunit 10

MacromoleculeName: Transcription initiation factor TFIID subunit 10 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 23.042186 KDa
SequenceString: MDFEEDYDAE FDDNQEGQLE TPFPSVAGAD DGDNDNDDSV AENMKKKQKR EAVVDDGSEN AFGIPEFTRK DKTLEEILEM MDSTPPIIP DAVIDYYLTK NGFNVADVRV KRLLALATQK FVSDIAKDAY EYSRIRSSVA VSNANNSQAR ARQLLQGQQQ P GVQQISQQ ...String:
MDFEEDYDAE FDDNQEGQLE TPFPSVAGAD DGDNDNDDSV AENMKKKQKR EAVVDDGSEN AFGIPEFTRK DKTLEEILEM MDSTPPIIP DAVIDYYLTK NGFNVADVRV KRLLALATQK FVSDIAKDAY EYSRIRSSVA VSNANNSQAR ARQLLQGQQQ P GVQQISQQ QHQQNEKTTA SKVVLTVNDL SSAVAEYGLN IGRPDFYR

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Macromolecule #7: Transcriptional coactivator HFI1/ADA1

MacromoleculeName: Transcriptional coactivator HFI1/ADA1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.52998 KDa
SequenceString: MSAIQSPAPK PLQPTYPAAS PASTNAYMKP GLIGSPAVSN HTEPNNGNNE TAEPQGPNQR IDLGAMIEEL TSLLGKESWT KYAQIISLF ILGKLSRKEL SNELELVFSP SAASLEKSNT NHHHSLVRLH NQLLLGIFAN SLRENPLGRN GNESSWGFGN G SNNPNNKL ...String:
MSAIQSPAPK PLQPTYPAAS PASTNAYMKP GLIGSPAVSN HTEPNNGNNE TAEPQGPNQR IDLGAMIEEL TSLLGKESWT KYAQIISLF ILGKLSRKEL SNELELVFSP SAASLEKSNT NHHHSLVRLH NQLLLGIFAN SLRENPLGRN GNESSWGFGN G SNNPNNKL KRINKHNSQI EVYKKIVMSL PLNDRNRLKM ITKEAGKRGF IFCSVFQARL NNIPKIPIVT NPESLKRVKS NN LKTPLEW SQDIMNGFNV PLASESHSLP DTDSFYLRMV GIAREHGLVG TVDARCVELI SLALDQYLKN IIEFTIDTVR YRR KKYSDY YDLNESGLYK SVSEMAADKR DAKIKQLDDD KNEDECADEA KSINNGNNSS KDDIGDISMS SITKAGEAVN EELH ENRTI SLTNEDIYDS LSIFPNLVEP SGSYYALTNL GLVNDDELVD MKSNIDDLPD FLNEKPTFTP LDERNVGTRH ELNWL IKGI LTED

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Macromolecule #8: Transcription initiation factor TFIID subunit 12

MacromoleculeName: Transcription initiation factor TFIID subunit 12 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 61.144379 KDa
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

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Macromolecule #9: Transcriptional activator SPT7

MacromoleculeName: Transcriptional activator SPT7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 152.813828 KDa
SequenceString: MTERIPIKNY QRTNAKALLK LTEKLFNKNF FDLYLTSQQL VVLEYLLSIS SEEDKLKAWD YFLKGNIALN VEKSFPLTQE EEHHGAVSP AVDTRSDDVS SQTIKDNNNT NTNTSISNEN HVENEIEDKG DNAIANEDNF VNNDESDNVE EDLFKLDLED L KQQISGTR ...String:
MTERIPIKNY QRTNAKALLK LTEKLFNKNF FDLYLTSQQL VVLEYLLSIS SEEDKLKAWD YFLKGNIALN VEKSFPLTQE EEHHGAVSP AVDTRSDDVS SQTIKDNNNT NTNTSISNEN HVENEIEDKG DNAIANEDNF VNNDESDNVE EDLFKLDLED L KQQISGTR FIGNLSLKIR YVLWQCAIDY IYCDRNEFGD ENDTEYTLLD VEEKEEEEIG KNEKPQNKEG ISKFAEDEDY DD EDENYDE DSTDVKNVDD PPKNLDSISS SNIEIDDERR LVLNISISKE TLSKLKTNNV EEIMGNWNKI YHSFEYDKET MIK RLKLEE SDKMIEKGKK KRSRSDLEAA TDEQDRENTN DEPDTNQKLP TPEGSTFSDT GNKRPKQSNL DLTVNLGIEN LSLK HLLSS IQQKKSQLGI SDYELKHLIM DVRKNRSKWT SDERIGQEEL YEACEKVVLE LRNYTEHSTP FLNKVSKREA PNYHQ IIKK SMDLNTVLKK LKSFQYDSKQ EFVDDIMLIW KNCLTYNSDP SHFLRGHAIA MQKKSLQLIR MIPNITIRNR ADLEKE IED MEKDKDYELD EEEEVAGSGR KGLNMGAHML AKENGKVSEK DSSKTVKDEA PTNDDKLTSV IPEGEKEKDK TASSTVT VH ENVNKNEIKE NGKNEEQDMV EESSKTEDSS KDADAAKKDT EDGLQDKTAE NKEAGENNEE EEDDDDEDED EDMVDSQS Y LLEKDDDRDD LEISVWKTVT AKVRAEICLK RTEYFKNGKL NSDSEAFLKN PQRMKRFDQL FLEYKEQKAL ESYRQKIEQ NSIMKNGFGT VLKQEDDDQL QFHNDHSLNG NEAFEKQPND IELDDTRFLQ EYDISNAIPD IVYEGVNTKT LDKMEDASVD RMLQNGINK QSRFLANKDL GLTPKMNQNI TLIQQIRHIC HKISLIRMLQ SPLSAQNSRS NPNAFLNNHI YNYTIIDDSL D IDPVSQLP THDYKNNREL IWKFMHKNIS KVAMANGFET AHPSAINMLT EIAGDYLSNL IKTLKLHHET NSLNRGTNVE ML QTTLLEN GINRPDDLFS YVESEFGKKT KKLQDIKQKL ESFLRALLRP TLQELSERNF EDESQSFFTG DFASELTGED FFG FRELGL EKEFGVLSSS VPLQLLTTQF QTVDGETKVQ AKKIQPEESD SIVYKKITKG MLDAGSFWNT LLPLLQKDYE RSKA YIAKQ SKSSANDKTS MTSTEDNSFA LLEEDQFVSK KTATKARLPP TGKISTTYKK KPIASAFILP EEDLENDVKA DPTTT VNAK VGAENDGDSS LFLRTPQPLD PLDMDDAFDD TNMGSNSSFS LSLPRLNQ

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Macromolecule #10: SAGA-associated factor 73

MacromoleculeName: SAGA-associated factor 73 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 72.976688 KDa
SequenceString: MRSGDAEIKG IKPKVIEEYS LSQGSGPSND SWKSLMSSAK DTPLQYDHMN RESLKKYFNP NAQLIEDPLD KPIQYRVCEK CGKPLALTA IVDHLENHCA GASGKSSTDP RDESTRETIR NGVESTGRNN NDDDNSNDNN NDDDDDDDND DNEDDDDADD D DDNSNGAN ...String:
MRSGDAEIKG IKPKVIEEYS LSQGSGPSND SWKSLMSSAK DTPLQYDHMN RESLKKYFNP NAQLIEDPLD KPIQYRVCEK CGKPLALTA IVDHLENHCA GASGKSSTDP RDESTRETIR NGVESTGRNN NDDDNSNDNN NDDDDDDDND DNEDDDDADD D DDNSNGAN YKKNDSSFNP LKRSTSMESA NTPNMDTKRS KTGTPQTFSS SIKKQKKVKQ RNPTEKHLID FNKQCGVELP EG GYCARSL TCKSHSMGAK RAVSGRSKPY DVLLADYHRE HQTKIGAAAE KRAKQQELQK LQKQIQKEQK KHTQQQKQGQ RSK QRNVNG GKSAKNGGKS TVHNGNNINE IGHVNLTPEE ETTQVLNGVS RSFPLPLEST VLSSVRYRTK YFRMREMFAS SFSV KPGYT SPGYGAIHSR VGCLDLDRTT DYKFRVRTPQ PINHLTNQNL NPKQIQRLQQ QRALQAQLLS QQQQQQQQQQ QHHSP QAQA QASTQQPTQG MVPNHFPGGA TNSSFNANVS SKQIQQQQQQ QQHKSQDTGL TPLEIQSQQQ KLRQQQLQQQ KFEAAA SYL ANATKLMQES NQDSHLSGTH NNNSSKNGNN NLMTMKASIS SPNTSVNSIQ SPPSVNSVNG SGQGVSTGIN VSGNNGR IE VGIGNSVNPY NGRIN

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Macromolecule #11: unassigned sequence

MacromoleculeName: unassigned sequence / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 11.03505 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAA

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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: 42.45 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 27602
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-6t9k:
SAGA Core module

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