+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16713 | |||||||||
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Title | Local refinement map of TFIIIC TauB-DNA monomer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TFIIIC / 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 / 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 / rRNA transcription / tRNA transcription by RNA polymerase III / transcription by RNA polymerase III / enzyme activator activity / histone acetyltransferase activity / histone acetyltransferase / ribonucleoprotein complex / nucleolus / mitochondrion / DNA binding / nucleoplasm / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wolfram SD / Mathias G / Luis H / Thomas H / Sebastian E / Christoph M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16713.map.gz | 244.8 MB | EMDB map data format | |
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Header (meta data) | emd-16713-v30.xml emd-16713.xml | 23.5 KB 23.5 KB | Display Display | EMDB header |
Images | emd_16713.png | 61.9 KB | ||
Masks | emd_16713_msk_1.map | 421.9 MB | Mask map | |
Others | emd_16713_additional_1.map.gz emd_16713_half_map_1.map.gz emd_16713_half_map_2.map.gz | 210.6 MB 390.9 MB 390.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16713 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16713 | HTTPS FTP |
-Related structure data
Related structure data | 8cliMC 8cljC 8clkC 8cllC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16713.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16713_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_16713_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16713_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16713_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TFIIIC tauB-DNA monomer
Entire | Name: TFIIIC tauB-DNA monomer |
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Components |
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-Supramolecule #1: TFIIIC tauB-DNA monomer
Supramolecule | Name: TFIIIC tauB-DNA monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: General transcription factor 3C polypeptide 1
Macromolecule | Name: General transcription factor 3C polypeptide 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 244.200719 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: General transcription factor 3C polypeptide 4
Macromolecule | Name: General transcription factor 3C polypeptide 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 92.093195 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #3: General transcription factor 3C polypeptide 2
Macromolecule | Name: General transcription factor 3C polypeptide 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 102.612453 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #4: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.819942 KDa |
Sequence | String: (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) |
-Macromolecule #5: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.7179 KDa |
Sequence | String: (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) |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / In silico model: Alphafold2 model |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35379 |