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- EMDB-10817: Structure of the TFIIIC subcomplex tauA -

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Basic information

Entry
Database: EMDB / ID: EMD-10817
TitleStructure of the TFIIIC subcomplex tauA
Map data
Sample
  • Complex: TFIIIC subcomplex tauA
    • Protein or peptide: Transcription factor tau 131 kDa subunit
    • Protein or peptide: Transcription factor tau 95 kDa subunit,Transcription factor tau 95 kDa subunit
    • Protein or peptide: Transcription factor tau 55 kDa subunit
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 / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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 / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Tetratricopeptide repeat / Histidine phosphatase superfamily / 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 55 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVorlaender MK / Muller CW
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the TFIIIC subcomplex τA provides insights into RNA polymerase III pre-initiation complex formation.
Authors: Matthias K Vorländer / Anna Jungblut / Kai Karius / Florence Baudin / Helga Grötsch / Jan Kosinski / Christoph W Müller /
Abstract: Transcription factor (TF) IIIC is a conserved eukaryotic six-subunit protein complex with dual function. It serves as a general TF for most RNA polymerase (Pol) III genes by recruiting TFIIIB, but it ...Transcription factor (TF) IIIC is a conserved eukaryotic six-subunit protein complex with dual function. It serves as a general TF for most RNA polymerase (Pol) III genes by recruiting TFIIIB, but it is also involved in chromatin organization and regulation of Pol II genes through interaction with CTCF and condensin II. Here, we report the structure of the S. cerevisiae TFIIIC subcomplex τA, which contains the most conserved subunits of TFIIIC and is responsible for recruitment of TFIIIB and transcription start site (TSS) selection at Pol III genes. We show that τA binding to its promoter is auto-inhibited by a disordered acidic tail of subunit τ95. We further provide a negative-stain reconstruction of τA bound to the TFIIIB subunits Brf1 and TBP. This shows that a ruler element in τA achieves positioning of TFIIIB upstream of the TSS, and suggests remodeling of the complex during assembly of TFIIIB by TFIIIC.
History
DepositionApr 2, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6yj6
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10817.png

Downloads & links

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Map

FileDownload / File: emd_10817.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.041 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.16542615 - 0.283146
Average (Standard dev.)-0.00016718963 (±0.0053780037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.300312.300312.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1650.283-0.000

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Supplemental data

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Half map: #1

Fileemd_10817_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_10817_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 subcomplex tauA

EntireName: TFIIIC subcomplex tauA
Components
  • Complex: TFIIIC subcomplex tauA
    • Protein or peptide: Transcription factor tau 131 kDa subunit
    • Protein or peptide: Transcription factor tau 95 kDa subunit,Transcription factor tau 95 kDa subunit
    • Protein or peptide: Transcription factor tau 55 kDa subunit

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Supramolecule #1: TFIIIC subcomplex tauA

SupramoleculeName: TFIIIC subcomplex tauA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Generated by co-expression of subunits in insect cells
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: Hi 5 cells
Molecular weightTheoretical: 245 KDa

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Macromolecule #1: Transcription factor tau 131 kDa subunit

MacromoleculeName: Transcription factor tau 131 kDa subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 120.746969 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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

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Macromolecule #2: Transcription factor tau 95 kDa subunit,Transcription factor tau ...

MacromoleculeName: Transcription factor tau 95 kDa subunit,Transcription factor tau 95 kDa subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 77.363664 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHENL YFQSMPVEEP LATLSSIPDS SADQAPPLIA DEFTLDLPRI PSLELPLNVS TKHSSIQKAI KMCGGIEKVK EAFKEHGPI ESQHGLQLYL NDDTDSDGSK SYFNEHPVIG KRVPFRDESV ILKVTMPKGT LSKNNNSVKD SIKSLKDSNK L RVTPVSIV ...String:
MHHHHHHENL YFQSMPVEEP LATLSSIPDS SADQAPPLIA DEFTLDLPRI PSLELPLNVS TKHSSIQKAI KMCGGIEKVK EAFKEHGPI ESQHGLQLYL NDDTDSDGSK SYFNEHPVIG KRVPFRDESV ILKVTMPKGT LSKNNNSVKD SIKSLKDSNK L RVTPVSIV DNTIKFREMS DFQIKLDNVP SAREFKSSFG SLEWNNFKSF VNSVPDNDSQ PQENIGNLIL DRSVKIPSTD FQ LPPPPKL SMVGFPLLYK YKANPFAKKK KNGVTEVKGT YIKNYQLFVH DLSDKTVIPS QAHEQVLYDF EVAKKTKVYP GTK SDSKFY ESLEECLKIL RELFARRPIW VKRHLDGIVP KKIHHTMKIA LALISYRFTM GPWRNTYIKF GIDPRSSVEY AQYQ TEYFK IERKLLSSPI VKKNVPKPPP LVFESDTPGG IDSRFKFDGK RIPWYLMLQI DLLIGEPNIA EVFHNVEYLD KANEL TGWF KELDLVKIRR IVKYELGCMV QGNYEYNKYK LKYFKTMLFV KESMVPENKN SEEGMGVNTN KDADGDINMD AGSQMS SNA IEEDKGIAAG DDFDDNGAIT EEPDDAALEN EEMDTDQNLK VPASIDDDVD DVDADEEEQE SFDVKTASFQ DIINKIA KL DPKTAETMKS ELKGFVDEVD L(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Transcription factor tau 55 kDa subunit

MacromoleculeName: Transcription factor tau 55 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 49.198898 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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

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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

Concentration1.3 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES, 5 mM DTT, 75 mM NaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco Easygglow instrument
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 2, Blot time 4.
Details4 mM CHAPSO added prior to freezing

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-36 / Number grids imaged: 1 / Number real images: 5824 / Average exposure time: 48.73 sec. / Average electron dose: 1.35 e/Å2 / Details: collected 8 frames per hole using beam shift
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 702583 / Details: BoxNet2_20180918 was used for particle picking
CTF correctionSoftware - Name: Warp (ver. 1.06)
Startup modelType of model: INSILICO MODEL / In silico model: obtained with Relion
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 254700
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6yj6:
Structure of the TFIIIC subcomplex tauA

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