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- EMDB-16715: TFIIIC TauA complex map -

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Basic information

Entry
Database: EMDB / ID: EMD-16715
TitleTFIIIC TauA complex map
Map data
Sample
  • Complex: TFIIIC TauA subcomplex
    • Protein or peptide: General transcription factor 3C polypeptide 1
    • Protein or peptide: General transcription factor 3C polypeptide 3
    • Protein or peptide: General transcription factor 3C polypeptide 5
    • Protein or peptide: General transcription factor 3C polypeptide 6
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 / skeletal muscle cell differentiation / tRNA 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 / skeletal muscle cell differentiation / tRNA transcription by RNA polymerase III / rRNA transcription / transcription by RNA polymerase III / fibrillar center / nuclear membrane / nuclear body / ribonucleoprotein complex / nucleolus / DNA binding / nucleoplasm / membrane
Similarity search - Function
TFIIIC subunit GTF3C6-like / 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 ...TFIIIC subunit GTF3C6-like / 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 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
General transcription factor 3C polypeptide 1 / General transcription factor 3C polypeptide 6 / General transcription factor 3C polypeptide 5 / General transcription factor 3C polypeptide 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16715.png

Downloads & links

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Map

FileDownload / File: emd_16715.map.gz / Format: CCP4 / Size: 166.4 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 352 pix.
= 289.344 Å		0.82 Å/pix.
x 352 pix.
= 289.344 Å		0.82 Å/pix.
x 352 pix.
= 289.344 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: 0.2
Minimum - Maximum-3.6346633 - 5.180893
Average (Standard dev.)0.005058167 (±0.08223427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 289.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16715_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16715_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16715_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 : TFIIIC TauA subcomplex

EntireName: TFIIIC TauA subcomplex
Components
  • Complex: TFIIIC TauA subcomplex
    • Protein or peptide: General transcription factor 3C polypeptide 1
    • Protein or peptide: General transcription factor 3C polypeptide 3
    • Protein or peptide: General transcription factor 3C polypeptide 5
    • Protein or peptide: General transcription factor 3C polypeptide 6

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Supramolecule #1: TFIIIC TauA subcomplex

SupramoleculeName: TFIIIC TauA subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 330 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: 1 / 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 3

MacromoleculeName: General transcription factor 3C polypeptide 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.387969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSGFSPELID YLEGKISFEE FERRREERKT REKKSLQEKG KLSAEENPDD SEVPSSSGIN STKSQDKDVN EGETSDGVRK SVHKVFASM LGENEDDEEE EEEEEEEEEE EETPEQPTAG DVFVLEMVLN RETKKMMKEK RPRSKLPRAL RGLMGEANIR F ARGEREEA ...String:
MSGFSPELID YLEGKISFEE FERRREERKT REKKSLQEKG KLSAEENPDD SEVPSSSGIN STKSQDKDVN EGETSDGVRK SVHKVFASM LGENEDDEEE EEEEEEEEEE EETPEQPTAG DVFVLEMVLN RETKKMMKEK RPRSKLPRAL RGLMGEANIR F ARGEREEA ILMCMEIIRQ APLAYEPFST LAMIYEDQGD MEKSLQFELI AAHLNPSDTE EWVRLAEMSL EQDNIKQAIF CY TKALKYE PTNVRYLWER SSLYEQMGDH KMAMDGYRRI LNLLSPSDGE RFMQLARDMA KSYYEANDVT SAINIIDEAF SKH QGLVSM EDVNIAAELY ISNKQYDKAL EIITDFSGIV LEKKTSEEGT SEENKAPENV TCTIPDGVPI DITVKLMVCL VHLN ILEPL NPLLTTLVEQ NPEDMGDLYL DVAEAFLDVG EYNSALPLLS ALVCSERYNL AVVWLRHAEC LKALGYMERA AESYG KVVD LAPLHLDARI SLSTLQQQLG QPEKALEALE PMYDPDTLAQ DANAAQQELK LLLHRSTLLF SQGKMYGYVD TLLTML AML LKVAMNRAQV CLISSSKSGE RHLYLIKVSR DKISDSNDQE SANCDAKAIF AVLTSVLTKD DWWNLLLKAI YSLCDLS RF QEAELLVDSS LEYYSFYDDR QKRKELEYFG LSAAILDKNF RKAYNYIRIM VMENVNKPQL WNIFNQVTMH SQDVRHHR F CLRLMLKNPE NHALCVLNGH NAFVSGSFKH ALGQYVQAFR THPDEPLYSF CIGLTFIHMA SQKYVLRRHA LIVQGFSFL NRYLSLRGPC QESFYNLGRG LHQLGLIHLA IHYYQKALEL PPLVVEGIEL DQLDLRRDIA YNLSLIYQSS GNTGMAQTLL YTYCSI

UniProtKB: General transcription factor 3C polypeptide 3

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Macromolecule #3: General transcription factor 3C polypeptide 5

MacromoleculeName: General transcription factor 3C polypeptide 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.46882 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHENL YFQGMAAEAA DLGLGAAVPV ELRRERRMVC VEYPGVVRDV AKMLPTLGGE EGVSRIYADP TKRLELYFRP KDPYCHPVC ANRFSTSSLL LRIRKRTRRQ KGVLGTEAHS EVTFDMEILG IISTIYKFQG MSDFQYLAVH TEAGGKHTSM Y DKVLMLRP ...String:
MHHHHHHENL YFQGMAAEAA DLGLGAAVPV ELRRERRMVC VEYPGVVRDV AKMLPTLGGE EGVSRIYADP TKRLELYFRP KDPYCHPVC ANRFSTSSLL LRIRKRTRRQ KGVLGTEAHS EVTFDMEILG IISTIYKFQG MSDFQYLAVH TEAGGKHTSM Y DKVLMLRP EKEAFFHQEL PLYIPPPIFS RLDAPVDYFY RPETQHREGY NNPPISGENL IGLSRARRPH NAIFVNFEDE EV PKQPLEA AAQTWRRVCT NPVDRKVEEE LRKLFDIRPI WSRNAVKANI SVHPDKLKVL LPFIAYYMIT GPWRSLWIRF GYD PRKNPD AKIYQVLDFR IRCGMKHGYA PSDLPVKAKR STYNYSLPIT VKKTSSQLVT MHDLKQGLGP SGTSGARKPA SSKY KLKDS VYIFREGALP PYRQMFYQLC DLNVEELQKI IHRNDGAENS CTERDGWCLP KTSDELRDTM SLMIRQTIRS KRPAL FSSS AKADGGKEQL TYESGEDEED EEEEEEEEED FKPSDGSENE METEILDYV

UniProtKB: General transcription factor 3C polypeptide 5

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Macromolecule #4: General transcription factor 3C polypeptide 6

MacromoleculeName: General transcription factor 3C polypeptide 6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.0696 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAADERSP EDGEDEEEEE QLVLVELSGI IDSDFLSKCE NKCKVLGIDT ERPILQVDSC VFAGEYEDTL GTCVIFEENV EHADTEGNN KTVLKYKCHT MKKLSMTRTL LTEKKEGEEN IGGVEWLQIK DNDFSYRPNM ICNFLHENED EEVVASAPDK S LELEEEEI ...String:
MAAAADERSP EDGEDEEEEE QLVLVELSGI IDSDFLSKCE NKCKVLGIDT ERPILQVDSC VFAGEYEDTL GTCVIFEENV EHADTEGNN KTVLKYKCHT MKKLSMTRTL LTEKKEGEEN IGGVEWLQIK DNDFSYRPNM ICNFLHENED EEVVASAPDK S LELEEEEI QMNDSSNLSC EQEKPMHLEI EDSGPLIDIP SETEGSVFME TQMLP

UniProtKB: General transcription factor 3C polypeptide 6

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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
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 6 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.8 e/Å2
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55079

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