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- EMDB-71457: TBP/TFIIE/DNA of PIC-Med-SWI/SNF -

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Basic information

Entry
Database: EMDB / ID: EMD-71457
TitleTBP/TFIIE/DNA of PIC-Med-SWI/SNF
Map data
Sample
  • Complex: TBP/TFIIE/DNA of PIC-Med-SWI/SNF
    • DNA: promoter DNA
    • Protein or peptide: TATA-box-binding protein
    • DNA: promoter DNA
    • Protein or peptide: Transcription initiation factor IIE subunit beta
    • Protein or peptide: Transcription initiation factor IIE subunit alpha
    • Protein or peptide: Transcription initiation factor IIB
    • Protein or peptide: Transcription initiation factor IIF subunit beta
    • Protein or peptide: Transcription initiation factor IIA large subunit
    • Protein or peptide: Transcription initiation factor IIA subunit 2
  • Ligand: ZINC ION
KeywordsSWI/SNF / PIC / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


TFIIA-class transcription factor complex binding / transcription open complex formation at RNA polymerase II promoter / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIIB complex / transcription factor TFIIA complex ...TFIIA-class transcription factor complex binding / transcription open complex formation at RNA polymerase II promoter / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIIB complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / transcription preinitiation complex / transcription factor TFIID complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II general transcription initiation factor activity / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / RNA polymerase II complex binding / positive regulation of transcription initiation by RNA polymerase II / nucleolar large rRNA transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / transcription by RNA polymerase II / transcription coregulator activity / disordered domain specific binding / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nucleotide binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Tfa2 E-tether / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain ...: / Tfa2 E-tether / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
TATA-box-binding protein / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIE subunit beta / Transcription initiation factor IIF subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsYang C / Nagai S / Chen D-H
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure of TBP/TFIIE/DNA of PIC-Med-SWI/SNF
Authors: Yang C / Nagai S / Chen D-H
History
DepositionJun 26, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71457.png

Downloads & links

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Map

FileDownload / File: emd_71457.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.)
1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0266
Minimum - Maximum-0.12103287 - 0.20539847
Average (Standard dev.)0.00017191142 (±0.0035677957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71457_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71457_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71457_half_map_1.map
Projections & Slices
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Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71457_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

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Sample components

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Entire : TBP/TFIIE/DNA of PIC-Med-SWI/SNF

EntireName: TBP/TFIIE/DNA of PIC-Med-SWI/SNF
Components
  • Complex: TBP/TFIIE/DNA of PIC-Med-SWI/SNF
    • DNA: promoter DNA
    • Protein or peptide: TATA-box-binding protein
    • DNA: promoter DNA
    • Protein or peptide: Transcription initiation factor IIE subunit beta
    • Protein or peptide: Transcription initiation factor IIE subunit alpha
    • Protein or peptide: Transcription initiation factor IIB
    • Protein or peptide: Transcription initiation factor IIF subunit beta
    • Protein or peptide: Transcription initiation factor IIA large subunit
    • Protein or peptide: Transcription initiation factor IIA subunit 2
  • Ligand: ZINC ION

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Supramolecule #1: TBP/TFIIE/DNA of PIC-Med-SWI/SNF

SupramoleculeName: TBP/TFIIE/DNA of PIC-Med-SWI/SNF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2 MDa

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Macromolecule #1: promoter DNA

MacromoleculeName: promoter DNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.78955 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DG)(DA)(DA)(DA)(DA)(DC) (DA)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DG) (DG)(DG)(DC)(DT)(DC)(DT)(DA)(DC)(DA) (DT)(DT)(DC)(DA)(DT)(DT)(DT)(DT)(DT)(DT) (DC) (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DA)

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Macromolecule #3: promoter DNA

MacromoleculeName: promoter DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.771523 KDa
SequenceString:
(DT)(DC)(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DA) (DA)(DA)(DA)(DA)(DA)(DT)(DG)(DA)(DA)(DT) (DG)(DT)(DA)(DG)(DA)(DG)(DC)(DC)(DC) (DT)(DT)(DT)(DT)(DT)(DA)(DT)(DA)(DT)(DG) (DT) (DT)(DT)(DT)(DC)(DA)(DC)(DC)(DG)

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Macromolecule #2: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.042275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF ...String:
MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF PIRLEGLAFS HGTFSSYEPE LFPGLIYRMV KPKIVLLIFV SGKIVLTGAK QREEIYQAFE AIYPVLSEFR KM

UniProtKB: TATA-box-binding protein

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Macromolecule #4: Transcription initiation factor IIE subunit beta

MacromoleculeName: Transcription initiation factor IIE subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.050434 KDa
SequenceString: MSKNRDPLLA NLNAFKSKVK SAPVIAPAKV GQKKTNDTVI TIDGNTRKRT ASERAQENTL NSAKNPVLVD IKKEAGSNSS NAISLDDDD DDEDFGSSPS KKVRPGSIAA AALQANQTDI SKSHDSSKLL WATEYIQKKG KPVLVNELLD YLSMKKDDKV I ELLKKLDR ...String:
MSKNRDPLLA NLNAFKSKVK SAPVIAPAKV GQKKTNDTVI TIDGNTRKRT ASERAQENTL NSAKNPVLVD IKKEAGSNSS NAISLDDDD DDEDFGSSPS KKVRPGSIAA AALQANQTDI SKSHDSSKLL WATEYIQKKG KPVLVNELLD YLSMKKDDKV I ELLKKLDR IEFDPKKGTF KYLSTYDVHS PSELLKLLRS QVTFKGISCK DLKDGWPQCD ETINQLEEDS KILVLRTKKD KT PRYVWYN SGGNLKCIDE EFVKMWENVQ LPQFAELPRK LQDLGLKPAS VDPATIKRQT KRVEVKKKRQ RKGKITNTHM TGI LKDYSH RV

UniProtKB: Transcription initiation factor IIE subunit beta

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Macromolecule #5: Transcription initiation factor IIE subunit alpha

MacromoleculeName: Transcription initiation factor IIE subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 54.804809 KDa
SequenceString: MDRPIDDIVK NLLKFVVRGF YGGSFVLVLD AILFHSVLAE DDLKQLLSIN KTELGPLIAR LRSDRLISIH KQREYPPNSK SVERVYYYV KYPHAIDAIK WKVHQVVQRL KDDLDKNSEP NGYMCPICLT KYTQLEAVQL LNFDRTEFLC SLCDEPLVED D SGKKNKEK ...String:
MDRPIDDIVK NLLKFVVRGF YGGSFVLVLD AILFHSVLAE DDLKQLLSIN KTELGPLIAR LRSDRLISIH KQREYPPNSK SVERVYYYV KYPHAIDAIK WKVHQVVQRL KDDLDKNSEP NGYMCPICLT KYTQLEAVQL LNFDRTEFLC SLCDEPLVED D SGKKNKEK QDKLNRLMDQ IQPIIDSLKK IDDSRIEENT FEIALARLIP PQNQSHAAYT YNPKKGSTMF RPGDSAPLPN LM GTALGND SSRRAGANSQ ATLHINITTA SDEVAQRELQ ERQAEEKRKQ NAVPEWHKQS TIGKTALGRL DNEEEFDPVV TAS AMDSIN PDNEPAQETS YQNNRTLTEQ EMEERENEKT LNDYYAALAK KQAKLNKEEE EEEEEEEDEE EEEEEEMEDV MDDN DETAR ENALEDEFED VTDTAGTAKT ESNTSNDVKQ ESINDKTEDA VNATATASGP SANAKPNDGD DDDDDDDDEM DIEFE DV

UniProtKB: Transcription initiation factor IIE subunit alpha

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Macromolecule #6: Transcription initiation factor IIB

MacromoleculeName: Transcription initiation factor IIB / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.25734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMTRESIDKR AGRRGPNLNI VLTCPECKVY PPKIVERFSE GDVVCALCGL VLSDKLVDTR SEWRTFSNDD HNGDDPSRVG EASNPLLDG NNLSTRIGKG ETTDMRFTKE LNKAQGKNVM DKKDNEVQAA FAKITMLCDA AELPKIVKDC AKEAYKLCHD E KTLKGKSM ...String:
MMTRESIDKR AGRRGPNLNI VLTCPECKVY PPKIVERFSE GDVVCALCGL VLSDKLVDTR SEWRTFSNDD HNGDDPSRVG EASNPLLDG NNLSTRIGKG ETTDMRFTKE LNKAQGKNVM DKKDNEVQAA FAKITMLCDA AELPKIVKDC AKEAYKLCHD E KTLKGKSM ESIMAASILI GCRRAEVART FKEIQSLIHV KTKEFGKTLN IMKNILRGKS EDGFLKIDTD NMSGAQNLTY IP RFCSHLG LPMQVTTSAE YTAKKCKEIK EIAGKSPITI AVVSIYLNIL LFQIPITAAK VGQTLQVTEG TIKSGYKILY EHR DKLVDP QLIANGVVSL DNLPGVEKK

UniProtKB: Transcription initiation factor IIB

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Macromolecule #7: Transcription initiation factor IIF subunit beta

MacromoleculeName: Transcription initiation factor IIF subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 46.684492 KDa
SequenceString: MSSGSAGAPA LSNNSTNSVA KEKSGNISGD EYLSQEEEVF DGNDIENNET KVYEESLDLD LERSNRQVWL VRLPMFLAEK WRDRNNLHG QELGKIRINK DGSKITLLLN ENDNDSIPHE YDLELTKKVV ENEYVFTEQN LKKYQQRKKE LEADPEKQRQ A YLKKQERE ...String:
MSSGSAGAPA LSNNSTNSVA KEKSGNISGD EYLSQEEEVF DGNDIENNET KVYEESLDLD LERSNRQVWL VRLPMFLAEK WRDRNNLHG QELGKIRINK DGSKITLLLN ENDNDSIPHE YDLELTKKVV ENEYVFTEQN LKKYQQRKKE LEADPEKQRQ A YLKKQERE EELKKKQQQQ KRRNNRKKFN HRVMTDRDGR DRYIPYVKTI PKKTAIVGTV CHECQVMPSM NDPNYHKIVE QR RNIVKLN NKERITTLDE TVGVTMSHTG MSMRSDNSNF LKVGREKAKS NIKSIRMPKK EILDYLFKLF DEYDYWSLKG LKE RTRQPE AHLKECLDKV ATLVKKGPYA FKYTLRPEYK KLKEEERKAT LGELADEQTG SAGDNAQGDA EADLEDEIEM EDVV

UniProtKB: Transcription initiation factor IIF subunit beta

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Macromolecule #8: Transcription initiation factor IIA large subunit

MacromoleculeName: Transcription initiation factor IIA large subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.230805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNAEASRVY EIIVESVVNE VREDFENAGI DEQTLQDLKN IWQKKLTETK VTTFSWDNQF NEGNINGVQN DLNFNLATPG VNSSEFNIK EENTGNEGLI LPNINSNNNI PHSGETNINT NTVEATNNSG ATLNTNTSGN TNADVTSQPK IEVKPEIELT I NNANITTV ...String:
MSNAEASRVY EIIVESVVNE VREDFENAGI DEQTLQDLKN IWQKKLTETK VTTFSWDNQF NEGNINGVQN DLNFNLATPG VNSSEFNIK EENTGNEGLI LPNINSNNNI PHSGETNINT NTVEATNNSG ATLNTNTSGN TNADVTSQPK IEVKPEIELT I NNANITTV ENIDDESEKK DDEEKEEDVE KTRKEKEQIE QVKLQAKKEK RSALLDTDEV GSELDDSDDD YLISEGEEDG PD ENLMLCL YDKVTRTKAR WKCSLKDGVV TINRNDYTFQ KAQVEAEWV

UniProtKB: Transcription initiation factor IIA large subunit

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Macromolecule #9: Transcription initiation factor IIA subunit 2

MacromoleculeName: Transcription initiation factor IIA subunit 2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.47307 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAVPGYYELY RRSTIGNSLV DALDTLISDG RIEASLAMRV LETFDKVVAE TLKDNTQSKL TVKGNLDTYG FCDDVWTFIV KNCQVTVED SHRDASQNGS GDSQSVISVD KLRIVACNSK KSE

UniProtKB: Transcription initiation factor IIA subunit 2

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 7.5
Details: 40 mM Hepes-KOH pH 7.5, 100 mM potassium acetate, 2 mM magnesium acetate and 5 mM DTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.0 sec. / Average electron dose: 40.8 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 382004
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9pb8:
TBP/TFIIE/DNA of PIC-Med-SWI/SNF

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