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- EMDB-53937: Cryo-EM structure of the human SAGA co-activator complex -

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Basic information

Entry
Database: EMDB / ID: EMD-53937
TitleCryo-EM structure of the human SAGA co-activator complex
Map dataComposite map of human SAGA
Sample
  • Complex: SAGA
    • Protein or peptide: x 13 types
KeywordsTranscription co-activator / Lysine acetyltransferase / complex / TRANSCRIPTION
Function / homology
Function and homology information


SAGA-type complex / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / Swr1 complex ...SAGA-type complex / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / Swr1 complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / maintenance of protein location in nucleus / splicing factor binding / regulation of double-strand break repair / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2-type spliceosomal complex / RNA polymerase binding / SAGA complex / U2 snRNP / transcription preinitiation complex / precatalytic spliceosome / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / limb development / nucleus organization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / regulation of RNA splicing / histone deacetylase complex / mRNA Splicing - Minor Pathway / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / U2 snRNA binding / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / positive regulation of double-strand break repair via homologous recombination / catalytic step 2 spliceosome / gastrulation / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / visual perception / TBP-class protein binding / RNA splicing / nuclear estrogen receptor binding / male germ cell nucleus / spliceosomal complex / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / promoter-specific chromatin binding / G1/S transition of mitotic cell cycle / mRNA splicing, via spliceosome / Formation of the beta-catenin:TCF transactivating complex / negative regulation of protein catabolic process / mRNA transcription by RNA polymerase II / microtubule cytoskeleton organization / autophagy / multicellular organism growth / nuclear matrix / cytoplasmic ribonucleoprotein granule / transcription corepressor activity / nucleosome / HATs acetylate histones / microtubule cytoskeleton / positive regulation of cell growth / regulation of apoptotic process / transcription by RNA polymerase II / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / nuclear speck / protein stabilization / chromatin remodeling / protein heterodimerization activity / focal adhesion / apoptotic process / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II
Similarity search - Function
STAGA complex 65 subunit gamma / : / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. ...STAGA complex 65 subunit gamma / : / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Transcription initiation factor IID, subunit 13 / : / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / Bromodomain transcription factors and PHD domain containing proteins / Transcription initiation factor TAFII31 / Bromodomain associated / Bromodomain associated domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / : / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / 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 / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Splicing factor 3B subunit 5 ...Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Splicing factor 3B subunit 5 / Transcription initiation factor TFIID subunit 9B / Transformation/transcription domain-associated protein / TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsDamilot M / Ben-Shem A / Papai G
Funding support France, 2 items
OrganizationGrant numberCountry
La ligue contre le cancer France
Agence Nationale de la Recherche (ANR)ANR-ATAC France
CitationJournal: Sci Adv / Year: 2026
Title: Insights into the structure and evolution of the human SAGA complex by affinity-ligand purification.
Authors: Mylène Damilot / Thomas Schoeps / Laszlo Tora / Patrick Schultz / Luc Lebeau / Gabor Papai / Adam Ben-Shem /
Abstract: Human SAGA is a 20-subunit transcriptional coactivator. Compared with yeast, metazoan SAGA uniquely incorporates a 150-kDa splicing-factor module (SPL), also present in U2 small nuclear ...Human SAGA is a 20-subunit transcriptional coactivator. Compared with yeast, metazoan SAGA uniquely incorporates a 150-kDa splicing-factor module (SPL), also present in U2 small nuclear ribonucleoprotein (U2snRNP). Metazoan gene duplication further specialized shared TFIID/SAGA subunits into SAGA-specific paralogs (TAF5L and TAF6L), but the functional consequences of this divergence are unknown. We report the structure of endogenous human SAGA purified via an affinity ligand from cells that were not disturbed by any genomic engineering tools. Our work reveals the high-resolution structure of SPL and the TAF6L HEAT repeat domain that provides the SPL with a docking surface. We elucidate how SPL and the HEAT repeats are incorporated into SAGA. We identify major structural differences between TAF6L/TAF5L and their canonical paralogs that enable SPL accommodation. SPL engages SAGA through a substantially smaller interface than in U2snRNP, despite sharing a deeply inserted helical motif. The seemingly weaker interaction of SPL with SAGA raises the possibility that SAGA relays this module to the splicing machinery.
History
DepositionJun 3, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53937.png

Downloads & links

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Map

FileDownload / File: emd_53937.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of human SAGA
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 408 pix.
= 408. Å		1 Å/pix.
x 408 pix.
= 408. Å		1 Å/pix.
x 408 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.81279236 - 29.832903000000002
Average (Standard dev.)0.055972446 (±0.63772225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SAGA

EntireName: SAGA
Components
  • Complex: SAGA
    • Protein or peptide: Splicing factor 3B subunit 3
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Transformation/transcription domain-associated protein
    • Protein or peptide: STAGA complex 65 subunit gamma
    • Protein or peptide: Transcription initiation factor TFIID subunit 9B
    • Protein or peptide: Transcription initiation factor TFIID subunit 12
    • Protein or peptide: Transcription initiation factor TFIID subunit 10
    • Protein or peptide: Transcription initiation protein SPT3 homolog
    • Protein or peptide: Transcriptional adapter 1
    • Protein or peptide: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
    • Protein or peptide: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
    • Protein or peptide: Transcription factor SPT20 homolog
    • Protein or peptide: Ataxin-7

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Supramolecule #1: SAGA

SupramoleculeName: SAGA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #13, #5-#6, #1, #7-#11, #3, #12, #2
Source (natural)Organism: Homo sapiens (human) / Strain: K562
Molecular weightTheoretical: 1.6 MDa

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Macromolecule #1: Transcription initiation factor TFIID subunit 9B

MacromoleculeName: Transcription initiation factor TFIID subunit 9B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.654861 KDa
SequenceString: MESGKMAPPK NAPRDALVMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKPNVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQK NQTPLPLIKP YAGPRLPPDR YCLTAPNYRL KSLIKKGPNQ GRLVPRLSVG AVSSKPTTPT I ATPQTVSV ...String:
MESGKMAPPK NAPRDALVMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKPNVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQK NQTPLPLIKP YAGPRLPPDR YCLTAPNYRL KSLIKKGPNQ GRLVPRLSVG AVSSKPTTPT I ATPQTVSV PNKVATPMSV TSQRFTVQIP PSQSTPVKPV PATTAVQNVL INPSMIGPKN ILITTNMVSS QNTANEANPL KR KHEDDDD NDIM

UniProtKB: Transcription initiation factor TFIID subunit 9B

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Macromolecule #2: Ataxin-7

MacromoleculeName: Ataxin-7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.597742 KDa
SequenceString: MSERAADDVR GEPRRAAAAA GGAAAAAARQ QQQQQQQQQP PPPQPQRQQH PPPPPRRTRP EDGGPGAAST SAAAMATVGE RRPLPSPEV MLGQSWNLWV EASKLPGKDG TELDESFKEF GKNREVMGLC REDMPIFGFC PAHDDFYLVV CNDCNQVVKP Q AFQSHYER ...String:
MSERAADDVR GEPRRAAAAA GGAAAAAARQ QQQQQQQQQP PPPQPQRQQH PPPPPRRTRP EDGGPGAAST SAAAMATVGE RRPLPSPEV MLGQSWNLWV EASKLPGKDG TELDESFKEF GKNREVMGLC REDMPIFGFC PAHDDFYLVV CNDCNQVVKP Q AFQSHYER RHSSSSKPPL AVPPTSVFSF FPSLSKSKGG SASGSNRSSS GGVLSASSSS SKLLKSPKEK LQLRGNTRPM HP IQQSRVP HGRIMTPSVK VEKIHPKMDG TLLKSAVGPT CPATVSSLVK PGLNCPSIPK PTLPSPGQIL NGKGLPAPPT LEK KPEDNS NNRKFLNKRL SEREFDPDIH CGVIDLDTKK PCTRSLTCKT HSLTQRRAVQ GRRKRFDVLL AEHKNKTREK ELIR HPDSQ QPPQPLRDPH PAPPRTSQEP HQNPHGVIPS ESKPFVASKP KPHTPSLPRP PGCPAQQGGS APIDPPPVHE SPHPP LPAT EPASRLSSEE GEGDDKEESV EKLDCHYSGH HPQPASFCTF GSRQIGRGYY VFDSRWNRLR CALNLMVEKH LNAQLW KKI PPVPSTTSPI STRIPHRTNS VPTSQCGVSY LAAATVSTSP VLLSSTCISP NSKSVPAHGT TLNAQPAASG AMDPVCS MQ SRQVSSSSSS PSTPSGLSSV PSSPMSRKPQ KLKSSKSLRP KESSGNSTNC QNASSSTSGG SGKKRKNSSP LLVHSSSS S SSSSSSSHSM ESFRKNCVAH SGPPYPSTVT SSHSIGLNCV TNKANAVNVR HDQSGRGPPT GSPAESIKRM SVMVNSSDS TLSLGPFIHQ SNELPVNSHG SFSHSHTPLD KLIGKKRKCS PSSSSINNSS SKPTKVAKVP AVNNVHMKHT GTIPGAQGLM NSSLLHQPK ARP

UniProtKB: Ataxin-7

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Macromolecule #3: TAF5-like RNA polymerase II p300/CBP-associated factor-associated...

MacromoleculeName: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.223047 KDa
SequenceString: MKRVRTEQIQ MAVSCYLKRR QYVDSDGPLK QGLRLSQTAE EMAANLTVQS ESGCANIVSA APCQAEPQQY EVQFGRLRNF LTDSDSQHS HEVMPLLYPL FVYLHLNLVQ NSPKSTVESF YSRFHGMFLQ NASQKDVIEQ LQTTQTIQDI LSNFKLRAFL D NKYVVRLQ ...String:
MKRVRTEQIQ MAVSCYLKRR QYVDSDGPLK QGLRLSQTAE EMAANLTVQS ESGCANIVSA APCQAEPQQY EVQFGRLRNF LTDSDSQHS HEVMPLLYPL FVYLHLNLVQ NSPKSTVESF YSRFHGMFLQ NASQKDVIEQ LQTTQTIQDI LSNFKLRAFL D NKYVVRLQ EDSYNYLIRY LQSDNNTALC KVLTLHIHLD VQPAKRTDYQ LYASGSSSRS ENNGLEPPDM PSPILQNEAA LE VLQESIK RVKDGPPSLT TICFYAFYNT EQLLNTAEIS PDSKLLAAGF DNSCIKLWSL RSKKLKSEPH QVDVSRIHLA CDI LEEEDD EDDNAGTEMK ILRGHCGPVY STRFLADSSG LLSCSEDMSI RYWDLGSFTN TVLYQGHAYP VWDLDISPYS LYFA SGSHD RTARLWSFDR TYPLRIYAGH LADVDCVKFH PNSNYLATGS TDKTVRLWSA QQGNSVRLFT GHRGPVLSLA FSPNG KYLA SAGEDQRLKL WDLASGTLYK ELRGHTDNIT SLTFSPDSGL IASASMDNSV RVWDIRNTYC SAPADGSSSE LVGVYT GQM SNVLSVQFMA CNLLLVTGIT QENQEH

UniProtKB: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L

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Macromolecule #4: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.718844 KDa
SequenceString: MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVI LEYQPSKNMF EKIHQETFGK SGCRRIVPGQ FLAVDPKGRA VMISAIEKQK LVYILNRDAA ARLTISSPLE A HKANTLVY ...String:
MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVI LEYQPSKNMF EKIHQETFGK SGCRRIVPGQ FLAVDPKGRA VMISAIEKQK LVYILNRDAA ARLTISSPLE A HKANTLVY HVVGVDVGFE NPMFACLEMD YEEADNDPTG EAAANTQQTL TFYELDLGLN HVVRKYSEPL EEHGNFLITV PG GSDGPSG VLICSENYIT YKNFGDQPDI RCPIPRRRND LDDPERGMIF VCSATHKTKS MFFFLAQTEQ GDIFKITLET DED MVTEIR LKYFDTVPVA AAMCVLKTGF LFVASEFGNH YLYQIAHLGD DDEEPEFSSA MPLEEGDTFF FQPRPLKNLV LVDE LDSLS PILFCQIADL ANEDTPQLYV ACGRGPRSSL RVLRHGLEVS EMAVSELPGN PNAVWTVRRH IEDEFDAYII VSFVN ATLV LSIGETVEEV TDSGFLGTTP TLSCSLLGDD ALVQVYPDGI RHIRADKRVN EWKTPGKKTI VKCAVNQRQV VIALTG GEL VYFEMDPSGQ LNEYTERKEM SADVVCMSLA NVPPGEQRSR FLAVGLVDNT VRIISLDPSD CLQPLSMQAL PAQPESL CI VEMGGTEKQD ELGERGSIGF LYLNIGLQNG VLLRTVLDPV TGDLSDTRTR YLGSRPVKLF RVRMQGQEAV LAMSSRSW L SYSYQSRFHL TPLSYETLEF ASGFASEQCP EGIVAISTNT LRILALEKLG AVFNQVAFPL QYTPRKFVIH PESNNLIII ETDHNAYTEA TKAQRKQQMA EEMVEAAGED ERELAAEMAA AFLNENLPES IFGAPKAGNG QWASVIRVMN PIQGNTLDLV QLEQNEAAF SVAVCRFSNT GEDWYVLVGV AKDLILNPRS VAGGFVYTYK LVNNGEKLEF LHKTPVEEVP AAIAPFQGRV L IGVGKLLR VYDLGKKKLL RKCENKHIAN YISGIQTIGH RVIVSDVQES FIWVRYKRNE NQLIIFADDT YPRWVTTASL LD YDTVAGA DKFGNICVVR LPPNTNDEVD EDPTGNKALW DRGLLNGASQ KAEVIMNYHV GETVLSLQKT TLIPGGSESL VYT TLSGGI GILVPFTSHE DHDFFQHVEM HLRSEHPPLC GRDHLSFRSY YFPVKNVIDG DLCEQFNSME PNKQKNVSEE LDRT PPEVS KKLEDIRTRY AF

UniProtKB: Splicing factor 3B subunit 3

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Macromolecule #5: Transformation/transcription domain-associated protein

MacromoleculeName: Transformation/transcription domain-associated protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 438.139531 KDa
SequenceString: MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQL RKLVLEIIHR IPTNEHLRPH TKNVLSVMFR FLETENEENV LICLRIIIEL HKQFRPPITQ EIHHFLDFVK Q IYKELPKV ...String:
MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQL RKLVLEIIHR IPTNEHLRPH TKNVLSVMFR FLETENEENV LICLRIIIEL HKQFRPPITQ EIHHFLDFVK Q IYKELPKV VNRYFENPQV IPENTVPPPE MVGMITTIAV KVNPEREDSE TRTHSIIPRG SLSLKVLAEL PIIVVLMYQL YK LNIHNVV AEFVPLIMNT IAIQVSAQAR QHKLYNKELY ADFIAAQIKT LSFLAYIIRI YQELVTKYSQ QMVKGMLQLL SNC PAETAH LRKELLIAAK HILTTELRNQ FIPCMDKLFD ESILIGSGYT ARETLRPLAY STLADLVHHV RQHLPLSDLS LAVQ LFAKN IDDESLPSSI QTMSCKLLLN LVDCIRSKSE QESGNGRDVL MRMLEVFVLK FHTIARYQLS AIFKKCKPQS ELGAV EAAL PGVPTAPAAP GPAPSPAPVP APPPPPPPPP PATPVTPAPV PPFEKQGEKD KEDKQTFQVT DCRSLVKTLV CGVKTI TWG ITSCKAPGEA QFIPNKQLQP KETQIYIKLV KYAMQALDIY QVQIAGNGQT YIRVANCQTV RMKEEKEVLE HFAGVFT MM NPLTFKEIFQ TTVPYMVERI SKNYALQIVA NSFLANPTTS ALFATILVEY LLDRLPEMGS NVELSNLYLK LFKLVFGS V SLFAAENEQM LKPHLHKIVN SSMELAQTAK EPYNYFLLLR ALFRSIGGGS HDLLYQEFLP LLPNLLQGLN MLQSGLHKQ HMKDLFVELC LTVPVRLSSL LPYLPMLMDP LVSALNGSQT LVSQGLRTLE LCVDNLQPDF LYDHIQPVRA ELMQALWRTL RNPADSISH VAYRVLGKFG GSNRKMLKES QKLHYVVTEV QGPSITVEFS DCKASLQLPM EKAIETALDC LKSANTEPYY R RQAWEVIK CFLVAMMSLE DNKHALYQLL AHPNFTEKTI PNVIISHRYK AQDTPARKTF EQALTGAFMS AVIKDLRPSA LP FVASLIR HYTMVAVAQQ CGPFLLPCYQ VGSQPSTAMF HSEENGSKGM DPLVLIDAIA ICMAYEEKEL CKIGEVALAV IFD VASIIL GSKERACQLP LFSYIVERLC ACCYEQAWYA KLGGVVSIKF LMERLPLTWV LQNQQTFLKA LLFVMMDLTG EVSN GAVAM AKTTLEQLLM RCATPLKDEE RAEEIVAAQE KSFHHVTHDL VREVTSPNST VRKQAMHSLQ VLAQVTGKSV TVIME PHKE VLQDMVPPKK HLLRHQPANA QIGLMEGNTF CTTLQPRLFT MDLNVVEHKV FYTELLNLCE AEDSALTKLP CYKSLP SLV PLRIAALNAL AACNYLPQSR EKIIAALFKA LNSTNSELQE AGEACMRKFL EGATIEVDQI HTHMRPLLMM LGDYRSL TL NVVNRLTSVT RLFPNSFNDK FCDQMMQHLR KWMEVVVITH KGGQRSDGNE SISECGRCPL SPFCQFEEMK ICSAIINL F HLIPAAPQTL VKPLLEVVMK TERAMLIEAG SPFREPLIKF LTRHPSQTVE LFMMEATLND PQWSRMFMSF LKHKDARPL RDVLAANPNR FITLLLPGGA QTAVRPGSPS TSTMRLDLQF QAIKIISIIV KNDDSWLASQ HSLVSQLRRV WVSENFQERH RKENMAATN WKEPKLLAYC LLNYCKRNYG DIELLFQLLR AFTGRFLCNM TFLKEYMEEE IPKNYSIAQK RALFFRFVDF N DPNFGDEL KAKVLQHILN PAFLYSFEKG EGEQLLGPPN PEGDNPESIT SVFITKVLDP EKQADMLDSL RIYLLQYATL LV EHAPHHI HDNNKNRNSK LRRLMTFAWP CLLSKACVDP ACKYSGHLLL AHIIAKFAIH KKIVLQVFHS LLKAHAMEAR AIV RQAMAI LTPAVPARME DGHQMLTHWT RKIIVEEGHT VPQLVHILHL IVQHFKVYYP VRHHLVQHMV SAMQRLGFTP SVTI EQRRL AVDLSEVVIK WELQRIKDQQ PDSDMDPNSS GEGVNSVSSS IKRGLSVDSA QEVKRFRTAT GAISAVFGRS QSLPG ADSL LAKPIDKQHT DTVVNFLIRV ACQVNDNTNT AGSPGEVLSR RCVNLLKTAL RPDMWPKSEL KLQWFDKLLM TVEQPN QVN YGNICTGLEV LSFLLTVLQS PAILSSFKPL QRGIAACMTC GNTKVLRAVH SLLSRLMSIF PTEPSTSSVA SKYEELE CL YAAVGKVIYE GLTNYEKATN ANPSQLFGTL MILKSACSNN PSYIDRLISV FMRSLQKMVR EHLNPQAASG STEATSGT S ELVMLSLELV KTRLAVMSME MRKNFIQAIL TSLIEKSPDA KILRAVVKIV EEWVKNNSPM AANQTPTLRE KSILLVKMM TYIEKRFPED LELNAQFLDL VNYVYRDETL SGSELTAKLE PAFLSGLRCA QPLIRAKFFE VFDNSMKRRV YERLLYVTCS QNWEAMGNH FWIKQCIELL LAVCEKSTPI GTSCQGAMLP SITNVINLAD SHDRAAFAMV THVKQEPRER ENSESKEEDV E IDIELAPG DQTSTPKTKE LSEKDIGNQL HMLTNRHDKF LDTLREVKTG ALLSAFVQLC HISTTLAEKT WVQLFPRLWK IL SDRQQHA LAGEISPFLC SGSHQVQRDC QPSALNCFVE AMSQCVPPIP IRPCVLKYLG KTHNLWFRST LMLEHQAFEK GLS LQIKPK QTTEFYEQES ITPPQQEILD SLAELYSLLQ EEDMWAGLWQ KRCKYSETAT AIAYEQHGFF EQAQESYEKA MDKA KKEHE RSNASPAIFP EYQLWEDHWI RCSKELNQWE ALTEYGQSKG HINPYLVLEC AWRVSNWTAM KEALVQVEVS CPKEM AWKV NMYRGYLAIC HPEEQQLSFI ERLVEMASSL AIREWRRLPH VVSHVHTPLL QAAQQIIELQ EAAQINAGLQ PTNLGR NNS LHDMKTVVKT WRNRLPIVSD DLSHWSSIFM WRQHHYQGKP TWSGMHSSSI VTAYENSSQH DPSSNNAMLG VHASASA II QYGKIARKQG LVNVALDILS RIHTIPTVPI VDCFQKIRQQ VKCYLQLAGV MGKNECMQGL EVIESTNLKY FTKEMTAE F YALKGMFLAQ INKSEEANKA FSAAVQMHDV LVKAWAMWGD YLENIFVKER QLHLGVSAIT CYLHACRHQN ESKSRKYLA KVLWLLSFDD DKNTLADAVD KYCIGVPPIQ WLAWIPQLLT CLVGSEGKLL LNLISQVGRV YPQAVYFPIR TLYLTLKIEQ RERYKSDPG PIRATAPMWR CSRIMHMQRE LHPTLLSSLE GIVDQMVWFR ENWHEEVLRQ LQQGLAKCYS VAFEKSGAVS D AKITPHTL NFVKKLVSTF GVGLENVSNV STMFSSAASE SLARRAQATA QDPVFQKLKG QFTTDFDFSV PGSMKLHNLI SK LKKWIKI LEAKTKQLPK FFLIEEKCRF LSNFSAQTAE VEIPGEFLMP KPTHYYIKIA RFMPRVEIVQ KHNTAARRLY IRG HNGKIY PYLVMNDACL TESRREERVL QLLRLLNPCL EKRKETTKRH LFFTVPRVVA VSPQMRLVED NPSSLSLVEI YKQR CAKKG IEHDNPISRY YDRLATVQAR GTQASHQVLR DILKEVQSNM VPRSMLKEWA LHTFPNATDY WTFRKMFTIQ LALIG FAEF VLHLNRLNPE MLQIAQDTGK LNVAYFRFDI NDATGDLDAN RPVPFRLTPN ISEFLTTIGV SGPLTASMIA VARCFA QPN FKVDGILKTV LRDEIIAWHK KTQEDTSSPL SAAGQPENMD SQQLVSLVQK AVTAIMTRLH NLAQFEGGES KVNTLVA AA NSLDNLCRMD PAWHPWL

UniProtKB: Transformation/transcription domain-associated protein

+
Macromolecule #6: STAGA complex 65 subunit gamma

MacromoleculeName: STAGA complex 65 subunit gamma / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.243629 KDa
SequenceString: MNLQRYWGEI PISSSQTNRS SFDLLPREFR LVEVHDPPLH QPSANKPKPP TMLDIPSEPC SLTIHTIQLI QHNRRLRNLI ATAQAQNQQ QTEGVKTEES EPLPSCPGSP PLPDDLLPLD CKNPNAPFQI RHSDPESDFY RGKGEPVTEL SWHSCRQLLY Q AVATILAH ...String:
MNLQRYWGEI PISSSQTNRS SFDLLPREFR LVEVHDPPLH QPSANKPKPP TMLDIPSEPC SLTIHTIQLI QHNRRLRNLI ATAQAQNQQ QTEGVKTEES EPLPSCPGSP PLPDDLLPLD CKNPNAPFQI RHSDPESDFY RGKGEPVTEL SWHSCRQLLY Q AVATILAH AGFDCANESV LETLTDVAHE YCLKFTKLLR FAVDREARLG QTPFPDVMEQ VFHEVGIGSV LSLQKFWQHR IK DYHSYML QISKQLSEEY ERIVNPEKAT EDAKPVKIKE EPVSDITFPV SEELEADLAS GDQSLPMGVL GAQSERFPSN LEV EASPQA SSAEVNASPL WNLAHVKMEP QESEEGNVSG HGVLGSDVFE EPMSGMSEAG IPQSPDDSDS SYGSHSTDSL MGSS PVFNQ RCKKRMRKI

UniProtKB: STAGA complex 65 subunit gamma

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Macromolecule #7: Transcription initiation factor TFIID subunit 12

MacromoleculeName: Transcription initiation factor TFIID subunit 12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.948467 KDa
SequenceString:
MNQFGPSALI NLSNFSSIKP EPASTPPQGS MANSTAVVKI PGTPGAGGRL SPENNQVLTK KKLQDLVREV DPNEQLDEDV EEMLLQIAD DFIESVVTAA CQLARHRKSS TLEVKDVQLH LERQWNMWIP GFGSEEIRPY KKACTTEAHK QRMALIRKTT K K

UniProtKB: Transcription initiation factor TFIID subunit 12

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Macromolecule #8: Transcription initiation factor TFIID subunit 10

MacromoleculeName: Transcription initiation factor TFIID subunit 10 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.731248 KDa
SequenceString: MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN ...String:
MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN DALQHCKMKG TASGSSRSKS KDRKYTLTME DLTPALSEYG INVKKPHYFT

UniProtKB: Transcription initiation factor TFIID subunit 10

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Macromolecule #9: Transcription initiation protein SPT3 homolog

MacromoleculeName: Transcription initiation protein SPT3 homolog / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.840816 KDa
SequenceString: MNNTAASPMS TATSSSGRST GKSISFATEL QSMMYSLGDA RRPLHETAVL VEDVVHTQLI NLLQQAAEVS QLRGARVITP EDLLFLMRK DKKKLRRLLK YMFIRDYKSK IVKGIDEDDL LEDKLSGSNN ANKRQKIAQD FLNSIDQTGE LLAMFEDDEI D EVKQERME ...String:
MNNTAASPMS TATSSSGRST GKSISFATEL QSMMYSLGDA RRPLHETAVL VEDVVHTQLI NLLQQAAEVS QLRGARVITP EDLLFLMRK DKKKLRRLLK YMFIRDYKSK IVKGIDEDDL LEDKLSGSNN ANKRQKIAQD FLNSIDQTGE LLAMFEDDEI D EVKQERME RAERQTRIMD SAQYAEFCES RQLSFSKKAS KFRDWLDCSS MEIKPNVVAM EILAYLAYET VAQLVDLALL VR QDMVTKA GDPFSHAISA TFIQYHNSAE STAACGVEAH SDAIQPCHIR EAIRRYSHRI GPLSPFTNAY RRNGMAFLAC

UniProtKB: Transcription initiation protein SPT3 homolog

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Macromolecule #10: Transcriptional adapter 1

MacromoleculeName: Transcriptional adapter 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.432531 KDa
SequenceString: MATFVSELEA AKKNLSEALG DNVKQYWANL KLWFKQKISK EEFDLEAHRL LTQDNVHSHN DFLLAILTRC QILVSTPDGA GSLPWPGGS AAKPGKPKGK KKLSSVRQKF DHRFQPQNPL SGAQQFVAKD PQDDDDLKLC SHTMMLPTRG QLEGRMIVTA Y EHGLDNVT ...String:
MATFVSELEA AKKNLSEALG DNVKQYWANL KLWFKQKISK EEFDLEAHRL LTQDNVHSHN DFLLAILTRC QILVSTPDGA GSLPWPGGS AAKPGKPKGK KKLSSVRQKF DHRFQPQNPL SGAQQFVAKD PQDDDDLKLC SHTMMLPTRG QLEGRMIVTA Y EHGLDNVT EEAVSAVVYA VENHLKDILT SVVSRRKAYR LRDGHFKYAF GSNVTPQPYL KNSVVAYNNL IESPPAFTAP CA GQNPASH PPPDDAEQQA ALLLACSGDT LPASLPPVNM YDLFEALQVH REVIPTHTVY ALNIERIITK LWHPNHEELQ QDK VHRQRL AAKEGLLLC

UniProtKB: Transcriptional adapter 1

+
Macromolecule #11: TAF6-like RNA polymerase II p300/CBP-associated factor-associated...

MacromoleculeName: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.903289 KDa
SequenceString: MSEREERRFV EIPRESVRLM AESTGLELSD EVAALLAEDV CYRLREATQN SSQFMKHTKR RKLTVEDFNR ALRWSSVEAV CGYGSQEAL PMRPAREGEL YFPEDREVNL VELALATNIP KGCAETAVRV HVSYLDGKGN LAPQGSVPSA VSSLTDDLLK Y YHQVTRAV ...String:
MSEREERRFV EIPRESVRLM AESTGLELSD EVAALLAEDV CYRLREATQN SSQFMKHTKR RKLTVEDFNR ALRWSSVEAV CGYGSQEAL PMRPAREGEL YFPEDREVNL VELALATNIP KGCAETAVRV HVSYLDGKGN LAPQGSVPSA VSSLTDDLLK Y YHQVTRAV LGDDPQLMKV ALQDLQTNSK IGALLPYFVY VVSGVKSVSH DLEQLHRLLQ VARSLFRNPH LCLGPYVRCL VG SVLYCVL EPLAASINPL NDHWTLRDGA ALLLSHIFWT HGDLVSGLYQ HILLSLQKIL ADPVRPLCCH YGAVVGLHAL GWK AVERVL YPHLSTYWTN LQAVLDDYSV SNAQVKADGH KVYGAILVAV ERLLKMKAQA AEPNRGGPGG RGCRRLDDLP WDSL LFQES SSGGGAEPSF GSGLPLPPGG AGPEDPSLSV TLADIYRELY AFFGDSLATR FGTGQPAPTA PRPPGDKKEP AAAPD SVRK MPQLTASAIV SPHGDESPRG SGGGGPASAS GPAASESRPL PRVHRARGAP RQQGPGTGTR DVFQKSRFAP RGAPHF RFI IAGRQAGRRC RGRLFQTAFP APYGPSPASR YVQKLPMIGR TSRPARRWAL SDYSLYLPL

UniProtKB: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L

+
Macromolecule #12: Transcription factor SPT20 homolog

MacromoleculeName: Transcription factor SPT20 homolog / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.884875 KDa
SequenceString: MQQALELALD RAEYVIESAR QRPPKRKYLS SGRKSVFQKL YDLYIEECEK EPEVKKLRRN VNLLEKLVMQ ETLSCLVVNL YPGNEGYSL MLRGKNGSDS ETIRLPYEEG ELLEYLDAEE LPPILVDLLE KSQVNIFHCG CVIAEIRDYR QSSNMKSPGY Q SRHILLRP ...String:
MQQALELALD RAEYVIESAR QRPPKRKYLS SGRKSVFQKL YDLYIEECEK EPEVKKLRRN VNLLEKLVMQ ETLSCLVVNL YPGNEGYSL MLRGKNGSDS ETIRLPYEEG ELLEYLDAEE LPPILVDLLE KSQVNIFHCG CVIAEIRDYR QSSNMKSPGY Q SRHILLRP TMQTLICDVH SITSDNHKWT QEDKLLLESQ LILATAEPLC LDPSIAVTCT ANRLLYNKQK MNTRPMKRCF KR YSRSSLN RQQDLSHCPP PPQLRLLDFL QKRKERKAGQ HYDLKISKAG NCVDMWKRSP CNLAIPSEVD VEKYAKVEKS IKS DDSQPT VWPAHDVKDD YVFECEAGTQ YQKTKLTILQ SLGDPLYYGK IQPCKADEES DSQMSPSHSS TDDHSNWFII GSKT DAERV VNQYQELVQN EAKCPVKMSH SSSGSASLSQ VSPGKETDQT ETVSVQSSVL GKGVKHRPPP IKLPSSSGNS SSGNY FTPQ QTSSFLKSPT PPPSSKPSSI PRKSSVDLNQ VSMLSPAALS PASSSQRTTA TQVMANSAGL NFINVVGSVC GAQALM SGS NPMLGCNTGA ITPAGINLSG LLPSGGLLPN ALPSAMQAAS QAGVPFGLKN TSSLRPLNLL QLPGGSLIFN TLQQQQQ QL SQFTPQQPQQ PTTCSPQQPG EQGSEQGSTS QEQALSAQQA AVINLTGVGS FMQSQAAVLS QLGSAENRPE QSLPQQRF Q LSSAFQQQQQ QIQQLRFLQH QMAMAAAAAQ TAQLHHHRHT GSQSKSKMKR GTPTTPKF

UniProtKB: Transcription factor SPT20 homolog

+
Macromolecule #13: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.149369 KDa
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

UniProtKB: Splicing factor 3B subunit 5

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1027610
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 272167
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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