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- EMDB-51228: yeast TFIIIC TauB subcomplex bound to a tRNA gene -

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Basic information

Entry
Database: EMDB / ID: EMD-51228
Titleyeast TFIIIC TauB subcomplex bound to a tRNA gene
Map data
Sample
  • Complex: Yeast TFIIIC TauB monomer bound to a tRNA gene
    • Protein or peptide: Transcription factor tau 138 kDa subunit
    • Protein or peptide: Transcription factor tau 91 kDa subunit
    • Protein or peptide: Transcription factor tau 60 kDa subunit
    • DNA: DNA (40-MER)
    • DNA: DNA (40-MER)
KeywordsBase-specific contacts / B-box / tRNA gene / DNA BINDING PROTEIN
Function / homology
Function and homology information


5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / protein localization to chromatin / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor tau subunit sfc3/Tfc3, C-terminal / : / Family of unknown function (DUF6581) / Transcription factor tau 138 kDa subunit, extended winged helix / Transcription factor IIIC, putative zinc-finger / : / Putative zinc-finger of transcription factor IIIC complex / B-block binding subunit of TFIIIC / Tfc3, extended winged-helix domain / Transcription facto Tfc3-like ...Transcription factor tau subunit sfc3/Tfc3, C-terminal / : / Family of unknown function (DUF6581) / Transcription factor tau 138 kDa subunit, extended winged helix / Transcription factor IIIC, putative zinc-finger / : / Putative zinc-finger of transcription factor IIIC complex / B-block binding subunit of TFIIIC / Tfc3, extended winged-helix domain / Transcription facto Tfc3-like / B-block binding subunit of TFIIIC / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Transcription factor tau 138 kDa subunit / Transcription factor tau 91 kDa subunit / Transcription factor tau 60 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsSeifert-Davila W / Girbig M / Hauptmann L / Hoffmann T / Eustermann S / Mueller C / Chaban A / Duss O / Baudin F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC.
Authors: Wolfram Seifert-Dávila / Anastasiia Chaban / Florence Baudin / Mathias Girbig / Luis Hauptmann / Thomas Hoffmann / Olivier Duss / Sebastian Eustermann / Christoph W Müller /
Abstract: Transcription of transfer RNA (tRNA) genes by RNA polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs of type II ...Transcription of transfer RNA (tRNA) genes by RNA polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs of type II gene promoters. However, the underlying mechanism has remained elusive, in part due to missing structural information for A-box recognition. In this study, we use single-particle cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) to reveal structural and real-time kinetic insights into how the 520-kDa yeast TFIIIC complex engages A-box and B-box DNA motifs in the context of a tRNA gene promoter. Cryo-EM structures of τA and τB subcomplexes bound to the A-box and B-box were obtained at 3.7 and 2.5 Å resolution, respectively, while cryo-EM single-particle mapping determined the specific distance and relative orientation of the τA and τB subcomplexes revealing a fully engaged state of TFIIIC. smFRET experiments show that overall recruitment and residence times of TFIIIC on a tRNA gene are primarily governed by B-box recognition, while footprinting experiments suggest a key role of τA and the A-box in TFIIIB and Pol III recruitment following TFIIIC recognition of type II promoters.
History
DepositionAug 1, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51228.png

Downloads & links

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Map

FileDownload / File: emd_51228.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.04 Å		0.82 Å/pix.
x 320 pix.
= 263.04 Å		0.82 Å/pix.
x 320 pix.
= 263.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.00966391 - 0.03340183
Average (Standard dev.)0.00006217974 (±0.00096598984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51228_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_51228_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 : Yeast TFIIIC TauB monomer bound to a tRNA gene

EntireName: Yeast TFIIIC TauB monomer bound to a tRNA gene
Components
  • Complex: Yeast TFIIIC TauB monomer bound to a tRNA gene
    • Protein or peptide: Transcription factor tau 138 kDa subunit
    • Protein or peptide: Transcription factor tau 91 kDa subunit
    • Protein or peptide: Transcription factor tau 60 kDa subunit
    • DNA: DNA (40-MER)
    • DNA: DNA (40-MER)

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Supramolecule #1: Yeast TFIIIC TauB monomer bound to a tRNA gene

SupramoleculeName: Yeast TFIIIC TauB monomer bound to a tRNA gene / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Transcription factor tau 138 kDa subunit

MacromoleculeName: Transcription factor tau 138 kDa subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 136.6025 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVLTIYPDEL VQIVSDKIAS NKGKITLNQL WDISGKYFDL SDKKVKQFVL SCVILKKDIE VYCDGAITTK NVTDIIGDAN HSYSVGITE DSLWTLLTGY TKKESTIGNS AFELLLEVAK SGEKGINTMD LAQVTGQDPR SVTGRIKKIN HLLTSSQLIY K GHVVKQLK ...String:
MVLTIYPDEL VQIVSDKIAS NKGKITLNQL WDISGKYFDL SDKKVKQFVL SCVILKKDIE VYCDGAITTK NVTDIIGDAN HSYSVGITE DSLWTLLTGY TKKESTIGNS AFELLLEVAK SGEKGINTMD LAQVTGQDPR SVTGRIKKIN HLLTSSQLIY K GHVVKQLK LKKFSHDGVD SNPYINIRDH LATIVEVVKR SKNGIRQIID LKRELKFDKE KRLSKAFIAA IAWLDEKEYL KK VLVVSPK NPAIKIRCVK YVKDIPDSKG SPSFEYDSNS ADEDSVSDSK AAFEDEDLVE GLDNFNATDL LQNQGLVMEE KED AVKNEV LLNRFYPLQN QTYDIADKSG LKGISTMDVV NRITGKEFQR AFTKSSEYYL ESVDKQKENT GGYRLFRIYD FEGK KKFFR LFTAQNFQKL TNAEDEISVP KGFDELGKSR TDLKTLNEDN FVALNNTVRF TTDSDGQDIF FWHGELKIPP NSKKT PNKN KRKRQVKNST NASVAGNISN PKRIKLEQHV STAQEPKSAE DSPSSNGGTV VKGKVVNFGG FSARSLRSLQ RQRAIL KVM NTIGGVAYLR EQFYESVSKY MGSTTTLDKK TVRGDVDLMV ESEKLGARTE PVSGRKIIFL PTVGEDAIQR YILKEKD SK KATFTDVIHD TEIYFFDQTE KNRFHRGKKS VERIRKFQNR QKNAKIKASD DAISKKSTSV NVSDGKIKRR DKKVSAGR T TVVVENTKED KTVYHAGTKD GVQALIRAVV VTKSIKNEIM WDKITKLFPN NSLDNLKKKW TARRVRMGHS GWRAYVDKW KKMLVLAIKS EKISLRDVEE LDLIKLLDIW TSFDEKEIKR PLFLYKNYEE NRKKFTLVRD DTLTHSGNDL AMSSMIQREI SSLKKTYTR KISASTKDLS KSQSDDYIRT VIRSILIESP STTRNEIEAL KNVGNESIDN VIMDMAKEKQ IYLHGSKLEC T DTLPDILE NRGNYKDFGV AFQYRCKVNE LLEAGNAIVI NQEPSDISSW VLIDLISGEL LNMDVIPMVR NVRPLTYTSR RF EIRTLTP PLIIYANSQT KLNTARKSAV KVPLGKPFSR LWVNGSGSIR PNIWKQVVTM VVNEIIFHPG ITLSRLQSRC REV LSLHEI SEICKWLLER QVLITTDFDG YWVNHNWYSI YESTENLYFQ SMSASAWSHP QFEKGGGSGG GSGGSAWSHP QFEK S

UniProtKB: Transcription factor tau 138 kDa subunit

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Macromolecule #2: Transcription factor tau 91 kDa subunit

MacromoleculeName: Transcription factor tau 91 kDa subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 76.48407 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHENLY FQGMAVIPAK KRGRPRKSVV AEVPYDSLAS PVSENSGSKR PRRNASKKAV ANFAQLVHAG RDDVINTTQV NNVDDTDDD DFVLNDEGDG EESDNVEIEF ENELESTKNE VADLNSSGSG ASVRPSGRRN TVQKLRLKKN STKNMKSSSP G SSLGQKGR ...String:
HHHHHHENLY FQGMAVIPAK KRGRPRKSVV AEVPYDSLAS PVSENSGSKR PRRNASKKAV ANFAQLVHAG RDDVINTTQV NNVDDTDDD DFVLNDEGDG EESDNVEIEF ENELESTKNE VADLNSSGSG ASVRPSGRRN TVQKLRLKKN STKNMKSSSP G SSLGQKGR PIRLLKDLSS ARDKIERIYG LNKEKLLLLA KVKEGFETSV FDFPFKNIQP DSPYFVCLDP PCKKESAYNK VI GDKNRTV YHEINKTEFE NMIKLRTKRL KLLIGEVDAE VSTGDKIEFP VLANGKRRGF IYNVGGLVTD IAWLNIEENT DIG KDIQYL AVAVSQYMDE PLNEHLEMFD KEKHSSCIQI FKMNTSTLHC VKVQTIVHSF GEVWDLKWHE GCHAPHLVGC LSFV SQEGT INFLEIIDNA TDVHVFKMCE KPSLTLSLAD SLITTFDFLS PTTVVCGFKN GFVAEFDLTD PEVPSFYDQV HDSYI LSVS TAYSDFEDTV VSTVAVDGYF YIFNPKDIAT TKTTVSRFRG SNLVPVVYCP QIYSYIYSDG ASSLRAVPSR AAFAVH PLV SRETTITAIG VSRLHPMVLA GSADGSLIIT NAARRLLHGI KNSSATQKSL RLWKWDYSIK DDKYRIDSSY EVYPLTV ND VSKAKIDAHG INITCTKWNE TSAGGKCYAF SNSAGLLTLE YLS

UniProtKB: Transcription factor tau 91 kDa subunit

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Macromolecule #3: Transcription factor tau 60 kDa subunit

MacromoleculeName: Transcription factor tau 60 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 67.755172 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKLLKDLLVD RKEFEDWKNN LTWARDGTLY LTTFPDISIG QPKYAKDINC NSKNLFHVKE FPLEFENKLD FELAQQNGLL NSQPVCYPR VCKPSPIDDW MAVLSNNGNV SVFKDNKMLT NLDSKGNLSS RTYHCFEWNP IESSIVVGNE DGELQFFSIR K NSENTPEF ...String:
MKLLKDLLVD RKEFEDWKNN LTWARDGTLY LTTFPDISIG QPKYAKDINC NSKNLFHVKE FPLEFENKLD FELAQQNGLL NSQPVCYPR VCKPSPIDDW MAVLSNNGNV SVFKDNKMLT NLDSKGNLSS RTYHCFEWNP IESSIVVGNE DGELQFFSIR K NSENTPEF YFESSIRLSD AGSKDWVTHI VWYEDVLVAA LSNNSVFSMT VSASSHQPVS RMIQNASRRK ITDLKIVDYK VV LTCPGYV HKIDLKNYSI SSLKTGSLEN FHIIPLNHEK ESTILLMSNK TSYKVLLEDE LHVTADNIIA PYLEKKFKKW STI WNEFNN YETTLVIHGI SLSPDGYSIA IVYDMERVAF KYKIASEQSF NIMFAPLYHT WTISERAVGL AWYQTYQIYN QSLP KLPEN FSMNKKLLNG NYPISLDFQS YLNALMKSEE MRIIMFLNMT IDKPSILSFL EALYEYAINK KSELTNSFDL ACVLS IAAI LKREAPIYNG TLLMKNSFLE ETFNLESFTA DPETVTSTTN NTWKRCGVTL LPILTTHVKI CPVSKQRVID IKRDDL NDY GWFTRGLLER FNEISVYCGT TLEVM

UniProtKB: Transcription factor tau 60 kDa subunit

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Macromolecule #4: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.358934 KDa
SequenceString:
(DG)(DC)(DC)(DG)(DA)(DT)(DG)(DA)(DA)(DA) (DC)(DC)(DC)(DT)(DG)(DG)(DT)(DT)(DC)(DG) (DA)(DT)(DT)(DC)(DT)(DA)(DG)(DG)(DA) (DG)(DA)(DT)(DG)(DG)(DC)(DA)(DT)(DT)(DT) (DT)

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Macromolecule #5: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.265904 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DT)(DG)(DC)(DC)(DA)(DT) (DC)(DT)(DC)(DC)(DT)(DA)(DG)(DA)(DA)(DT) (DC)(DG)(DA)(DA)(DC)(DC)(DA)(DG)(DG) (DG)(DT)(DT)(DT)(DC)(DA)(DT)(DC)(DG)(DG) (DC)

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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: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.6 e/Å2
Details: dataset1: 39.6 dataset2: 43.6 dataset3: 43.2 dataset4: 43.2 dataset5: 44.4
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Alphafol multimer V2.3.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 570437
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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