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- EMDB-51231: yeast TFIIIC TauA subcomplex bound to a tRNA gene -

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Basic information

Entry
Database: EMDB / ID: EMD-51231
Titleyeast TFIIIC TauA subcomplex bound to a tRNA gene
Map data
Sample
  • Complex: Yeast TFIIIC TauA monomer bound to a tRNA gene
    • Complex: Transcription factor tau
      • Protein or peptide: Transcription factor tau 138 kDa subunit
      • Protein or peptide: Transcription factor tau 131 kDa subunit
      • Protein or peptide: Transcription factor tau 95 kDa subunit
      • Protein or peptide: Transcription factor tau 55 kDa subunit
    • Complex: DNA
      • DNA: DNA (45-MER)
      • DNA: DNA (45-MER)
KeywordsA-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 Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / phosphatase activity / transcription by RNA polymerase III / protein localization to chromatin / mitochondrion / DNA binding / nucleoplasm ...5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / phosphatase activity / transcription by RNA polymerase III / protein localization to chromatin / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm
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 TFIIIC subunit Tfc7/tau55 / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor Tfc4/TFIIIC-102/Sfc4 / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain ...Transcription factor tau subunit sfc3/Tfc3, C-terminal / : / Family of unknown function (DUF6581) / Transcription factor tau 138 kDa subunit, extended winged helix / Transcription factor TFIIIC subunit Tfc7/tau55 / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor Tfc4/TFIIIC-102/Sfc4 / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain / Tau95 Triple barrel domain / B-block binding subunit of TFIIIC / Tfc3, extended winged-helix domain / Transcription facto Tfc3-like / B-block binding subunit of TFIIIC / : / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Transcription factor tau 95 kDa subunit / Transcription factor tau 131 kDa subunit / Transcription factor tau 138 kDa subunit / Transcription factor tau 55 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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: 2024
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 2, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_51231.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
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0093928445 - 0.026297655
Average (Standard dev.)0.000050821378 (±0.00061500823)
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: #2

Fileemd_51231_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_51231_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Yeast TFIIIC TauA monomer bound to a tRNA gene

EntireName: Yeast TFIIIC TauA monomer bound to a tRNA gene
Components
  • Complex: Yeast TFIIIC TauA monomer bound to a tRNA gene
    • Complex: Transcription factor tau
      • Protein or peptide: Transcription factor tau 138 kDa subunit
      • Protein or peptide: Transcription factor tau 131 kDa subunit
      • Protein or peptide: Transcription factor tau 95 kDa subunit
      • Protein or peptide: Transcription factor tau 55 kDa subunit
    • Complex: DNA
      • DNA: DNA (45-MER)
      • DNA: DNA (45-MER)

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

SupramoleculeName: Yeast TFIIIC TauA monomer bound to a tRNA gene / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Transcription factor tau

SupramoleculeName: Transcription factor tau / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
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 131 kDa subunit

MacromoleculeName: Transcription factor tau 131 kDa subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 120.746969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAGKLKKEQ QNQSAERESA DTGKVNDEDE EHLYGNIDDY KHLIQDEEYD DEDVPHDLQL SEDEYNSERD SSLLAEFSDY GEISEDDEE DFMNAIREAS NFKVKKKKKN DKGKSYGRQR KERVLDPEVA QLLSQANEAF VRNDLQVAER LFNEVIKKDA R NFAAYETL ...String:
MAAGKLKKEQ QNQSAERESA DTGKVNDEDE EHLYGNIDDY KHLIQDEEYD DEDVPHDLQL SEDEYNSERD SSLLAEFSDY GEISEDDEE DFMNAIREAS NFKVKKKKKN DKGKSYGRQR KERVLDPEVA QLLSQANEAF VRNDLQVAER LFNEVIKKDA R NFAAYETL GDIYQLQGRL NDCCNSWFLA AHLNASDWEF WKIVAILSAD LDHVRQAIYC FSRVISLNPM EWESIYRRSM LY KKTGQLA RALDGFQRLY MYNPYDANIL RELAILYVDY DRIEDSIELY MKVFNANVER REAILAALEN ALDSSDEESA AEG EDADEK EPLEQDEDRQ MFPDINWKKI DAKYKCIPFD WSSLNILAEL FLKLAVSEVD GIKTIKKCAR WIQRRESQTF WDHV PDDSE FDNRRFKNST FDSLLAAEKE KSYNIPIDIR VRLGLLRLNT DNLVEALNHF QCLYDETFSD VADLYFEAAT ALTRA EKYK EAIDFFTPLL SLEEWRTTDV FKPLARCYKE IESYETAKEF YELAIKSEPD DLDIRVSLAE VYYRLNDPET FKHMLV DVV EMRKHQVDET LHRISNEKSS NDTSDISSKP LLEDSKFRTF RKKKRTPYDA ERERIERERR ITAKVVDKYE KMKKFEL NS GLNEAKQASI WINTVSELVD IFSSVKNFFM KSRSRKFVGI LRRTKKFNTE LDFQIERLSK LAEGDSVFEG PLMEERVT L TSATELRGLS YEQWFELFME LSLVIAKYQS VEDGLSVVET AQEVNVFFQD PERVKMMKFV KLAIVLQMDD EEELAENLR GLLNQFQFNR KVLQVFMYSL CRGPSSLNIL SSTIQQKFFL RQLKAFDSCR YNTEVNGQAS ITNKEVYNPN KKSSPYLYYI YAVLLYSSR GFLSALQYLT RLEEDIPDDP MVNLLMGLSH IHRAMQRLTA QRHFQIFHGL RYLYRYHKIR KSLYTDLEKQ E ADYNLGRA FHLIGLVSIA IEYYNRVLEN YDDGKLKKHA AYNSIIIYQQ SGNVELADHL MEKYLSIRSG G

UniProtKB: Transcription factor tau 131 kDa subunit

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Macromolecule #3: Transcription factor tau 95 kDa subunit

MacromoleculeName: Transcription factor tau 95 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 69.066438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHENLY FQSMPVEEPL ATLSSIPDSS ADQAPPLIAD EFTLDLPRIP SLELPLNVST KHSSIQKAIK MCGGIEKVKE AFKEHGPIE SQHGLQLYLN DDTDSDGSKS YFNEHPVIGK RVPFRDESVI LKVTMPKGTL SKNNNSVKDS IKSLKDSNKL R VTPVSIVD ...String:
HHHHHHENLY FQSMPVEEPL ATLSSIPDSS ADQAPPLIAD EFTLDLPRIP SLELPLNVST KHSSIQKAIK MCGGIEKVKE AFKEHGPIE SQHGLQLYLN DDTDSDGSKS YFNEHPVIGK RVPFRDESVI LKVTMPKGTL SKNNNSVKDS IKSLKDSNKL R VTPVSIVD NTIKFREMSD FQIKLDNVPS AREFKSSFGS LEWNNFKSFV NSVPDNDSQP QENIGNLILD RSVKIPSTDF QL PPPPKLS MVGFPLLYKY KANPFAKKKK NGVTEVKGTY IKNYQLFVHD LSDKTVIPSQ AHEQVLYDFE VAKKTKVYPG TKS DSKFYE SLEECLKILR ELFARRPIWV KRHLDGIVPK KIHHTMKIAL ALISYRFTMG PWRNTYIKFG IDPRSSVEYA QYQT EYFKI ERKLLSSPIV KKNVPKPPPL VFESDTPGGI DSRFKFDGKR IPWYLMLQID LLIGEPNIAE VFHNVEYLDK ANELT GWFK ELDLVKIRRI VKYELGCMVQ GNYEYNKYKL KYFKTMLFVK ESMVPENKNS EEGMGVNTNK DADGDINMDA GSQMSS NAI EEDKGIAAGD DFDDNGAITE EPDDAALENE EMDTDQNLKV PAS

UniProtKB: Transcription factor tau 95 kDa subunit

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Macromolecule #4: Transcription factor tau 55 kDa subunit

MacromoleculeName: Transcription factor tau 55 kDa subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 49.198898 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVVNTIYIAR HGYRSNWLPE GPYPDPLTGI DSDVPLAEHG VQQAKELAHY LLSLDNQPEA AFASPFYRCL ETVQPIAKLL EIPVYLERG IGEWYRPDRK PVIPVPAGYE ILSKFFPGVI SQEWDSTLTP NEKGETEQEM YMRFKKFWPL FIERVEKEYP N VECILLVT ...String:
MVVNTIYIAR HGYRSNWLPE GPYPDPLTGI DSDVPLAEHG VQQAKELAHY LLSLDNQPEA AFASPFYRCL ETVQPIAKLL EIPVYLERG IGEWYRPDRK PVIPVPAGYE ILSKFFPGVI SQEWDSTLTP NEKGETEQEM YMRFKKFWPL FIERVEKEYP N VECILLVT HAASKIALGM SLLGYDNPRM SLNENGDKIR SGSCSLDKYE ILKKSYDTID ETDDQTSFTY IPFSDRKWVL TM NGNTEFL SSGEEMNWNF DCVAEAGSDA DIKKRQMTKK TSSPIPEADD QTEVETVYIS VDIPSGNYKE RTEIAKSAIL QYS GLETDA PLFRIGNRLY EGSWERLVGT ELAFPNAAHV HKKTAGLLSP TEENETTNAG QSKGSSTAND PNIQIQEEDV GLPD STNTS RDHTGDKEEV QSEKIYRIKE RIVLSNVRPM

UniProtKB: Transcription factor tau 55 kDa subunit

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Macromolecule #5: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.643719 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)

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Macromolecule #6: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.049344 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(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: 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114621
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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