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- PDB-8ffz: TFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene -

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Basic information

Entry
Database: PDB / ID: 8ffz
TitleTFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene
Components
  • (DNA (151-MER)) x 2
  • (Transcription factor ...) x 8
KeywordsTRANSCRIPTION/DNA / transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III core binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / TFIIA-class transcription factor complex binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding ...RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III core binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / TFIIA-class transcription factor complex binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / phosphatase activity / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / DNA-templated transcription initiation / disordered domain specific binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / 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 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 / 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 / : / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / C2H2-type zinc finger / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Tetratricopeptide repeat / Histidine phosphatase superfamily / TBP domain superfamily / Tetratricopeptide repeat / Zinc finger, C2H2 type / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / zinc finger / Zinc finger C2H2 type domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Tetratricopeptide repeats / Tetratricopeptide repeat / Zinc finger C2H2-type / Tetratricopeptide-like helical domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / TATA-box-binding protein / Transcription factor IIIB 70 kDa subunit / Transcription factor tau 95 kDa subunit / Transcription factor tau 131 kDa subunit / Transcription factor tau 138 kDa subunit / Transcription factor IIIA ...: / DNA / DNA (> 10) / DNA (> 100) / TATA-box-binding protein / Transcription factor IIIB 70 kDa subunit / Transcription factor tau 95 kDa subunit / Transcription factor tau 131 kDa subunit / Transcription factor tau 138 kDa subunit / Transcription factor IIIA / Transcription factor tau 91 kDa subunit / Transcription factor tau 60 kDa subunit / Transcription factor tau 55 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTalyzina, A. / He, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
American Cancer Society United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: Mol Cell / Year: 2023
Title: Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation.
Authors: Anna Talyzina / Yan Han / Chiranjib Banerjee / Susan Fishbain / Alexis Reyes / Reza Vafabakhsh / Yuan He /
Abstract: RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors ...RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here, we use cryoelectron microscopy (cryo-EM) to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Gene-specific factor TFIIIA interacts with DNA and acts as an adaptor for TFIIIC-promoter interactions. We also visualize DNA binding of TFIIIB subunits, Brf1 and TBP (TATA-box binding protein), which results in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA within the complex undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the transcription initiation complex assembly on the 5S rRNA promoter and allow us to directly compare Pol III and Pol II transcription adaptations.
#1: Journal: bioRxiv / Year: 2023
Title: Structural basis of TFIIIC-dependent RNA Polymerase III transcription initiation.
Authors: Anna Talyzina / Yan Han / Chiranjib Banerjee / Susan Fishbain / Alexis Reyes / Reza Vafabakhsh / Yuan He /
Abstract: RNA Polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors ...RNA Polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here we use cryo-electron microscopy to visualize the complex of TFIIIA and TFIIIC bound to the promoter. Brf1-TBP binding further stabilizes the DNA, resulting in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the mechanism of how the transcription initiation complex assembles on the 5S rRNA promoter, a crucial step in Pol III transcription regulation.
History
DepositionDec 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes / Item: _pdbx_validate_planes.type
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor IIIA
B: Transcription factor tau 138 kDa subunit
C: Transcription factor tau 131 kDa subunit
D: Transcription factor tau 95 kDa subunit
E: Transcription factor tau 91 kDa subunit
F: Transcription factor tau 60 kDa subunit
G: Transcription factor tau 55 kDa subunit
H: Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein
I: DNA (151-MER)
J: DNA (151-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)758,88919
Polymers758,30010
Non-polymers5899
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Negative stain
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription factor ... , 8 types, 8 molecules ABCDEFGH

#1: Protein Transcription factor IIIA / TFIIIA / Putative zinc finger protein 1


Mass: 52522.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PZF1, TFC2, TFIIIA, YPR186C, P9677.9 / Production host: Escherichia coli (E. coli) / References: UniProt: P39933
#2: Protein Transcription factor tau 138 kDa subunit / TFIIIC 138 kDa subunit / Transcription factor C subunit 3


Mass: 132313.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC3, TSV115, YAL001C, FUN24 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34111
#3: Protein Transcription factor tau 131 kDa subunit / TFIIIC 131 kDa subunit / Transcription factor C subunit 4


Mass: 120388.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC4, PCF1, YGR047C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33339
#4: Protein Transcription factor tau 95 kDa subunit / TFIIIC 95 kDa subunit / Transcription factor C subunit 1


Mass: 73649.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC1, YBR123C, YBR0919 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32367
#5: Protein Transcription factor tau 91 kDa subunit / TFIIIC 91 kDa subunit / Transcription factor C subunit 6


Mass: 74803.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC6, YDR362C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06339
#6: Protein Transcription factor tau 60 kDa subunit / TFIIIC 60 kDa subunit / Transcription factor C subunit 8


Mass: 67755.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC8, YPL007C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12308
#7: Protein Transcription factor tau 55 kDa subunit / TFIIIC 55 kDa subunit / Transcription factor C subunit 7


Mass: 49198.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC7, YOR110W, O3234, YOR3234w / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12415
#8: Protein Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein / TFIIIB / B-related factor 1 / BRF-1 / TATA sequence-binding protein / TBP / TATA-binding factor / ...TFIIIB / B-related factor 1 / BRF-1 / TATA sequence-binding protein / TBP / TATA-binding factor / TATA-box factor / Transcription factor D / Transcription initiation factor TFIID TBP subunit


Mass: 82097.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: BRF1, PCF4, TDS4, YGR246C, SPT15, BTF1, TBP1, YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P29056, UniProt: P13393

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DNA chain , 2 types, 2 molecules IJ

#9: DNA chain DNA (151-MER)


Mass: 52636.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822
#10: DNA chain DNA (151-MER)


Mass: 52934.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822

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Non-polymers , 1 types, 9 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TFIIIA-TFIIIC-Brf1-TBP complex bound to 5SrRNA gene / Type: COMPLEX / Entity ID: #1-#10 / Source: RECOMBINANT
Molecular weightValue: 810 kDa/nm / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.9
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
1Gautomatchparticle selection
2RELION3.1particle selection
5CTFFIND4CTF correction
8UCSF ChimeraX1.3model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5748589
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78512 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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