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- EMDB-16714: TFIIIC TauB-DNA dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-16714
TitleTFIIIC TauB-DNA dimer
Map data
Sample
  • Complex: TFIIIC tauB-DNA Dimer
    • Protein or peptide: General transcription factor 3C polypeptide 1
    • Protein or peptide: General transcription factor 3C polypeptide 4
    • Protein or peptide: General transcription factor 3C polypeptide 2
    • DNA: tDNA (35-MER)
    • DNA: tDNA (35-MER)
  • Ligand: ZINC ION
KeywordsTFIIIC / tRNA gene / B-Box promoter / DNA recognition / TRANSCRIPTION
Function / homology
Function and homology information


tRNA transcription / 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 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / rRNA transcription / transcription by RNA polymerase III ...tRNA transcription / 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 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / rRNA transcription / transcription by RNA polymerase III / tRNA transcription by RNA polymerase III / histone acetyltransferase activity / histone acetyltransferase / enzyme activator activity / ribonucleoprotein complex / nucleolus / mitochondrion / DNA binding / nucleoplasm / membrane
Similarity search - Function
Transcription factor IIIC, 90kDa subunit, N-terminal / General transcription factor 3C polypeptide 4 / Domain of unknown function DUF5921 / Transcription factor IIIC subunit delta bet-propeller domain / Domain of unknown function (DUF5921) / 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 factor IIIC, 90kDa subunit, N-terminal / General transcription factor 3C polypeptide 4 / Domain of unknown function DUF5921 / Transcription factor IIIC subunit delta bet-propeller domain / Domain of unknown function (DUF5921) / 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, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
General transcription factor 3C polypeptide 1 / General transcription factor 3C polypeptide 2 / General transcription factor 3C polypeptide 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWolfram SD / Mathias G / Luis H / Thomas H / Sebastian E / Christoph M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: Sci Adv / Year: 2023
Title: Structural insights into human TFIIIC promoter recognition.
Authors: Wolfram Seifert-Davila / Mathias Girbig / Luis Hauptmann / Thomas Hoffmann / Sebastian Eustermann / Christoph W Müller /
Abstract: Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB ...Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation.
History
DepositionFeb 16, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16714.png

Downloads & links

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Map

FileDownload / File: emd_16714.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 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: 0.6
Minimum - Maximum-3.3962228 - 5.808489
Average (Standard dev.)0.000002941929 (±0.11485468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16714_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_16714_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : TFIIIC tauB-DNA Dimer

EntireName: TFIIIC tauB-DNA Dimer
Components
  • Complex: TFIIIC tauB-DNA Dimer
    • Protein or peptide: General transcription factor 3C polypeptide 1
    • Protein or peptide: General transcription factor 3C polypeptide 4
    • Protein or peptide: General transcription factor 3C polypeptide 2
    • DNA: tDNA (35-MER)
    • DNA: tDNA (35-MER)
  • Ligand: ZINC ION

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Supramolecule #1: TFIIIC tauB-DNA Dimer

SupramoleculeName: TFIIIC tauB-DNA Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: General transcription factor 3C polypeptide 1

MacromoleculeName: General transcription factor 3C polypeptide 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 244.200719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDALESLLDE VALEGLDGLC LPALWSRLET RVPPFPLPLE PCTQEFLWRA LATHPGISFY EEPRERPDLQ LQDRYEEIDL ETGILESRR DPVALEDVYP IHMILENKDG IQGSCRYFKE RKNITNDIRT KSLQPRCTMV EAFDRWGKKL IIVASQAMRY R ALIGQEGD ...String:
MDALESLLDE VALEGLDGLC LPALWSRLET RVPPFPLPLE PCTQEFLWRA LATHPGISFY EEPRERPDLQ LQDRYEEIDL ETGILESRR DPVALEDVYP IHMILENKDG IQGSCRYFKE RKNITNDIRT KSLQPRCTMV EAFDRWGKKL IIVASQAMRY R ALIGQEGD PDLKLPDFSY CILERLGRSR WQGELQRDLH TTAFKVDAGK LHYHRKILNK NGLITMQSHV IRLPTGAQQH SI LLLLNRF HVDRRSKYDI LMEKLSVMLS TRTNHIETLG KLREELGLCE RTFKRLYQYM LNAGLAKVVS LRLQEIHPEC GPC KTKKGT DVMVRCLKLL KEFKRNDHDD DEDEEVISKT VPPVDIVFER DMLTQTYDLI ERRGTKGISQ AEIRVAMNVG KLEA RMLCR LLQRFKVVKG FMEDEGRQRT TKYISCVFAE ESDLSRQYQR EKARSELLTT VSLASMQEES LLPEGEDTFL SESDS EEER SSSKRRGRGS QKDTRASANL RPKTQPHHST PTKGGWKVVN LHPLKKQPPS FPGAAEERAC QSLASRDSLL DTSSVS EPN VSFVSHCADS NSGDIAVIEE VRMENPKESS SSLKTGRHSS GQDKPHETYR LLKRRNLIIE AVTNLRLIES LFTIQKM IM DQEKQEGVST KCCKKSIVRL VRNLSEEGLL RLYRTTVIQD GIKKKVDLVV HPSMDQNDPL VRSAIEQVRF RISNSSTA N RVKTSQPPVP QGEAEEDSQG KEGPSGSGDS QLSASSRSES GRMKKSDNKM GITPLRNYHP IVVPGLGRSL GFLPKMPRL RVVHMFLWYL IYGHPASNTV EKPSFISERR TIKQESGRAG VRPSSSGSAW EACSEAPSKG SQDGVTWEAE VELATETVYV DDASWMRYI PPIPVHRDFG FGWALVSDIL LCLPLSIFIQ IVQVSYKVDN LEEFLNDPLK KHTLIRFLPR PIRQQLLYKR R YIFSVVEN LQRLCYMGLL QFGPTEKFQD KDQVFIFLKK NAVIVDTTIC DPHYNLARSS RPFERRLYVL NSMQDVENYW FD LQCVCLN TPLGVVRCPR VRKNSSTDQG SDEEGSLQKE QESAMDKHNL ERKCAMLEYT TGSREVVDEG LIPGDGLGAA GLD SSFYGH LKRNWIWTSY IINQAKKENT AAENGLTVRL QTFLSKRPMP LSARGNSRLN IWGEARVGSE LCAGWEEQFE VDRE PSLDR NRRVRGGKSQ KRKRLKKDPG KKIKRKKKGE FPGEKSKRLR YHDEADQSAL QRMTRLRVTW SMQEDGLLVL CRIAS NVLN TKVKGPFVTW QVVRDILHAT FEESLDKTSH SVGRRARYIV KNPQAYLNYK VCLAEVYQDK ALVGDFMNRR GDYDDP KVC ANEFKEFVEK LKEKFSSALR NSNLEIPDTL QELFARYRVL AIGDEKDQTR KEDELNSVDD IHFLVLQNLI QSTLALS DS QMKSYQSFQT FRLYREYKDH VLVKAFMECQ KRSLVNRRRV NHTLGPKKNR ALPFVPMSYQ LSQTYYRIFT WRFPSTIC T ESFQFLDRMR AAGKLDQPDR FSFKDQDNNE PTNDMVAFSL DGPGGNCVAV LTLFSLGLIS VDVRIPEQII VVDSSMVEN EVIKSLGKDG SLEDDEDEED DLDEGVGGKR RSMEVKPAQA SHTNYLLMRG YYSPGIVSTR NLNPNDSIVV NSCQMKFQLR CTPVPARLR PAAAPLEELT MGTSCLPDTF TKLINPQENT CSLEEFVLQL ELSGYSPEDL TAALEILEAI IATGCFGIDK E ELRRRFSA LEKAGGGRTR TFADCIQALL EQHQVLEVGG NTARLVAMGS AWPWLLHSVR LKDREDADIQ REDPQARPLE GS SSEDSPP EGQAPPSHSP RGTKRRASWA SENGETDAEG TQMTPAKRPA LQDSNLAPSL GPGAEDGAEA QAPSPPPALE DTA AAGAAQ EDQEGVGEFS SPGQEQLSGQ AQPPEGSEDP RGFTESFGAA NISQAARERD CESVCFIGRP WRVVDGHLNL PVCK GMMEA MLYHIMTRPG IPESSLLRHY QGVLQPVAVL ELLQGLESLG CIRKRWLRKP RPVSLFSTPV VEEVEVPSSL DESPM AFYE PTLDCTLRLG RVFPHEVNWN KWIHLGGGSG GGSGGSLEVL FQGPGSGSDY KDDDDKGDYK DDDDKGDYKD DDDK

UniProtKB: General transcription factor 3C polypeptide 1

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Macromolecule #2: General transcription factor 3C polypeptide 4

MacromoleculeName: General transcription factor 3C polypeptide 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.093195 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNTADQARVG PADDGPAPSG EEEGEGGGEA GGKEPAADAA PGPSAAFRLM VTRREPAVKL QYAVSGLEPL AWSEDHRVSV STARSIAVL ELICDVHNPG QDLVIHRTSV PAPLNSCLLK VGSKTEVAEC KEKFAASKDP TVSQTFMLDR VFNPEGKALP P MRGFKYTS ...String:
MNTADQARVG PADDGPAPSG EEEGEGGGEA GGKEPAADAA PGPSAAFRLM VTRREPAVKL QYAVSGLEPL AWSEDHRVSV STARSIAVL ELICDVHNPG QDLVIHRTSV PAPLNSCLLK VGSKTEVAEC KEKFAASKDP TVSQTFMLDR VFNPEGKALP P MRGFKYTS WSPMGCDANG RCLLAALTMD NRLTIQANLN RLQWVQLVDL TEIYGERLYE TSYRLSKNEA PEGNLGDFAE FQ RRHSMQT PVRMEWSGIC TTQQVKHNNE CRDVGSVLLA VLFENGNIAV WQFQLPFVGK ESISSCNTIE SGITSPSVLF WWE YEHNNR KMSGLIVGSA FGPIKILPVN LKAVKGYFTL RQPVILWKEM DQLPVHSIKC VPLYHPYQKC SCSLVVAARG SYVF WCLLL ISKAGLNVHN SHVTGLHSLP IVSMTADKQN GTVYTCSSDG KVRQLIPIFT DVALKFEHQL IKLSDVFGSV RTHGI AVSP CGAYLAIITT EGMINGLHPV NKNYQVQFVT LKTFEEAAAQ LLESSVQNLF KQVDLIDLVR WKILKDKHIP QFLQEA LEK KIESSGVTYF WRFKLFLLRI LYQSMQKTPS EALWKPTHED SKILLVDSPG MGNADDEQQE EGTSSKQVVK QGLQERS KE GDVEEPTDDS LPTTGDAGGR EPMEEKLLEI QGKIEAVEMH LTREHMKRVL GEVYLHTWIT ENTSIPTRGL CNFLMSDE E YDDRTARVLI GHISKKMNKQ TFPEHCSLCK EILPFTDRKQ AVCSNGHIWL RCFLTYQSCQ SLIYRRCLLH DSIARHPAP EDPDWIKRLL QSPCPFCDSP VF

UniProtKB: General transcription factor 3C polypeptide 4

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Macromolecule #3: General transcription factor 3C polypeptide 2

MacromoleculeName: General transcription factor 3C polypeptide 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.612453 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHENL YFQGMDTCGV GYVALGEAGP VGNMTVVDSP GQEVLNQLDV KTSSEMTSAE ASVEMSLPTP LPGFEDSPDQ RRLPPEQES LSRLEQPDLS SEMSKVSKPR ASKPGRKRGG RTRKGPKRPQ QPNPPSAPLV PGLLDQSNPL STPMPKKRGR K SKAELLLL ...String:
MHHHHHHENL YFQGMDTCGV GYVALGEAGP VGNMTVVDSP GQEVLNQLDV KTSSEMTSAE ASVEMSLPTP LPGFEDSPDQ RRLPPEQES LSRLEQPDLS SEMSKVSKPR ASKPGRKRGG RTRKGPKRPQ QPNPPSAPLV PGLLDQSNPL STPMPKKRGR K SKAELLLL KLSKDLDRPE SQSPKRPPED FETPSGERPR RRAAQVALLY LQELAEELST ALPAPVSCPE GPKVSSPTKP KK IRQPAAC PGGEEVDGAP RDEDFFLQVE AEDVEESEGP SESSSEPEPV VPRSTPRGST SGKQKPHCRG MAPNGLPNHI MAP VWKCLH LTKDFREQKH SYWEFAEWIP LAWKWHLLSE LEAAPYLPQE EKSPLFSVQR EGLPEDGTLY RINRFSSITA HPER WDVSF FTGGPLWALD WCPVPEGAGA SQYVALFSSP DMNETHPLSQ LHSGPGLLQL WGLGTLQQES CPGNRAHFVY GIACD NGCI WDLKFCPSGA WELPGTPRKA PLLPRLGLLA LACSDGKVLL FSLPHPEALL AQQPPDAVKP AIYKVQCVAT LQVGSM QAT DPSECGQCLS LAWMPTRPHQ HLAAGYYNGM VVFWNLPTNS PLQRIRLSDG SLKLYPFQCF LAHDQAVRTL QWCKANS HF LVSAGSDRKI KFWDLRRPYE PINSIKRFLS TELAWLLPYN GVTVAQDNCY ASYGLCGIHY IDAGYLGFKA YFTAPRKG T VWSLSGSDWL GTIAAGDISG ELIAAILPDM ALNPINVKRP VERRFPIYKA DLIPYQDSPE GPDHSSASSG VPNPPKART YTETVNHHYL LFQDTDLGSF HDLLRREPML RMQEGEGHSQ LCLDRLQLEA IHKVRFSPNL DSYGWLVSGG QSGLVRIHFV RGLASPLGH RMQLESRAHF NAMFQPSSPT RRPGFSPTSH RLLPTP

UniProtKB: General transcription factor 3C polypeptide 2

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Macromolecule #4: tDNA (35-MER)

MacromoleculeName: tDNA (35-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.819942 KDa
SequenceString:
(DA)(DA)(DA)(DG)(DG)(DT)(DT)(DG)(DT)(DG) (DG)(DG)(DT)(DT)(DC)(DG)(DA)(DG)(DT)(DC) (DC)(DC)(DA)(DC)(DC)(DA)(DG)(DA)(DG) (DT)(DC)(DG)(DC)(DT)(DT)

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Macromolecule #5: tDNA (35-MER)

MacromoleculeName: tDNA (35-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.7179 KDa
SequenceString:
(DA)(DA)(DG)(DC)(DG)(DA)(DC)(DT)(DC)(DT) (DG)(DG)(DT)(DG)(DG)(DG)(DA)(DC)(DT)(DC) (DG)(DA)(DA)(DC)(DC)(DC)(DA)(DC)(DA) (DA)(DC)(DC)(DT)(DT)(DT)

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / 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: 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: 42.8 e/Å2
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: Alphafold2 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35379
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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