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- PDB-7z0o: Structure of transcription factor UAF in complex with TBP and 35S... -

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Basic information

Entry
Database: PDB / ID: 7z0o
TitleStructure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA
Components
  • (RNA polymerase I-specific transcription initiation factor ...) x 3
  • Histone H3
  • Histone H4
  • Non-template DNA
  • TATA-box-binding protein
  • Template DNA
  • Upstream activation factor subunit UAF30
KeywordsTRANSCRIPTION / Transcription Factor / Nucleolus / Histone Fold
Function / homology
Function and homology information


: / : / RNA polymerase I cis-regulatory region sequence-specific DNA binding / : / Regulation of TP53 Degradation / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / TFIIA-class transcription factor complex binding ...: / : / RNA polymerase I cis-regulatory region sequence-specific DNA binding / : / Regulation of TP53 Degradation / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / TFIIA-class transcription factor complex binding / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / rDNA binding / HDACs deacetylate histones / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / regulation of transcription by RNA polymerase III / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transcription factor TFIIA complex / replication fork protection complex / RNA polymerase I preinitiation complex assembly / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / 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 Pre-transcription Events / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / rRNA transcription / Estrogen-dependent gene expression / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / Ub-specific processing proteases / CENP-A containing nucleosome / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / structural constituent of chromatin / nucleosome / disordered domain specific binding / nucleosome assembly / chromatin organization / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
RNA polymerase I-specific transcription initiation factor Rrn10, Saccharomycetes / Rrn9 domain / RNA polymerase I-specific transcription initiation factor Rrn10 / RNA polymerase I-specific transcription initiation factor Rrn5 / UAF complex subunit Rrn10 / RNA polymerase I specific transcription initiation factor / DEK, C-terminal / DEK C terminal domain / SWIB domain / SWI complex, BAF60b domains ...RNA polymerase I-specific transcription initiation factor Rrn10, Saccharomycetes / Rrn9 domain / RNA polymerase I-specific transcription initiation factor Rrn10 / RNA polymerase I-specific transcription initiation factor Rrn5 / UAF complex subunit Rrn10 / RNA polymerase I specific transcription initiation factor / DEK, C-terminal / DEK C terminal domain / SWIB domain / SWI complex, BAF60b domains / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 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. / TBP domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / TATA-box-binding protein / RNA polymerase I-specific transcription initiation factor RRN10 / RNA polymerase I-specific transcription initiation factor RRN9 / Histone H3 / RNA polymerase I-specific transcription initiation factor RRN5 / Upstream activation factor subunit UAF30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBaudin, F. / Murciano, B. / Fung, H.K.H. / Fromm, S.A. / Mueller, C.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
CitationJournal: Sci Adv / Year: 2022
Title: Mechanism of RNA polymerase I selection by transcription factor UAF.
Authors: Florence Baudin / Brice Murciano / Herman K H Fung / Simon A Fromm / Simone Mattei / Julia Mahamid / Christoph W Müller /
Abstract: Preribosomal RNA is selectively transcribed by RNA polymerase (Pol) I in eukaryotes. The yeast transcription factor upstream activating factor (UAF) represses Pol II transcription and mediates Pol I ...Preribosomal RNA is selectively transcribed by RNA polymerase (Pol) I in eukaryotes. The yeast transcription factor upstream activating factor (UAF) represses Pol II transcription and mediates Pol I preinitiation complex (PIC) formation at the 35 ribosomal RNA gene. To visualize the molecular intermediates toward PIC formation, we determined the structure of UAF in complex with native promoter DNA and transcription factor TATA-box-binding protein (TBP). We found that UAF recognizes DNA using a hexameric histone-like scaffold with markedly different interactions compared with the nucleosome and the histone-fold-rich transcription factor IID (TFIID). In parallel, UAF positions TBP for Core Factor binding, which leads to Pol I recruitment, while sequestering it from DNA and Pol II/III-specific transcription factors. Our work thus reveals the structural basis of RNA Pol selection by a transcription factor.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H3
D: RNA polymerase I-specific transcription initiation factor RRN5
E: RNA polymerase I-specific transcription initiation factor RRN9
F: RNA polymerase I-specific transcription initiation factor RRN10
G: Upstream activation factor subunit UAF30
H: TATA-box-binding protein
N: Non-template DNA
T: Template DNA


Theoretical massNumber of molelcules
Total (without water)289,98310
Polymers289,98310
Non-polymers00
Water00
1


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

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Components

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Protein , 4 types, 5 molecules ACBGH

#1: Protein Histone H3


Mass: 15391.007 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61830
#2: Protein Histone H4


Mass: 11395.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02309
#6: Protein Upstream activation factor subunit UAF30 / Upstream activation factor 30 KDa subunit / p30


Mass: 26014.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: UAF30, YOR295W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08747
#7: Protein TATA-box-binding protein / TATA sequence-binding protein / TBP / TATA-binding factor / TATA-box factor / Transcription factor ...TATA sequence-binding protein / TBP / TATA-binding factor / TATA-box factor / Transcription factor D / Transcription initiation factor TFIID TBP subunit


Mass: 27237.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SPT15, BTF1, TBP1, YER148W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13393

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RNA polymerase I-specific transcription initiation factor ... , 3 types, 3 molecules DEF

#3: Protein RNA polymerase I-specific transcription initiation factor RRN5


Mass: 41873.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRN5, YLR141W, L3165, L9606.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02983
#4: Protein RNA polymerase I-specific transcription initiation factor RRN9


Mass: 42964.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRN9, YMR270C, YM8156.12C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53437
#5: Protein RNA polymerase I-specific transcription initiation factor RRN10


Mass: 16525.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRN10, YBL025W, YBL0426 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38204

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DNA chain , 2 types, 2 molecules NT

#8: DNA chain Non-template DNA


Mass: 47265.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 854429
#9: DNA chain Template DNA


Mass: 45924.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 854429

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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: Upstream Activating Factor (UAF) bound to TBP and promoter DNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameBuffer-ID
130 mMHEPES1
230 mMSodium Citrate1
3250 mMPotassium Chloride1
42 mMDTT1
50.1 %LMNG1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 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: 1900 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEM3.8image acquisition
4cryoSPARCCTF correction
5RELIONCTF correction
11cryoSPARCinitial Euler assignment
12RELIONinitial Euler assignment
13RELION3.1.2final Euler assignment
14RELION3.1.2classification
15RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193226 / Symmetry type: POINT

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