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- PDB-7ml3: General transcription factor TFIIH (weak binding) -

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Basic information

Entry
Database: PDB / ID: 7ml3
TitleGeneral transcription factor TFIIH (weak binding)
Components
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription and DNA repair factor IIH subunit ...) x 2
  • BJ4_G0050160.mRNA.1.CDS.1
  • General transcription and DNA repair factor IIH
  • RNA polymerase II transcription factor B subunit 2
  • Tfb1
  • non-template strand DNA
  • template strand DNA
KeywordsTRANSCRIPTION / PIC / TFIIH / ITC / RNA polymerase II
Function / homology
Function and homology information


regulation of mitotic recombination / RNA polymerase II promoter clearance / DNA translocase activity / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity ...regulation of mitotic recombination / RNA polymerase II promoter clearance / DNA translocase activity / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / 3'-5' DNA helicase activity / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / DNA duplex unwinding / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair 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 / Dual incision in TC-NER / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA helicase activity / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / DNA helicase / transcription by RNA polymerase II / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Bacterial type XPD DNA helicase, FeS cluster domain / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / RAD3/XPD family ...Bacterial type XPD DNA helicase, FeS cluster domain / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / RAD3/XPD family / Helicase XPB/Ssl2 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 type domain signature. / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / General transcription and DNA repair factor IIH helicase subunit XPD / RNA polymerase II transcription factor B subunit 2 / RNA polymerase II transcription factor B subunit 3 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsYang, C. / Fujiwara, R. / Kim, H.J. / Gorbea Colon, J.J. / Steimle, S. / Garcia, B.A. / Murakami, K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA196539 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG031862 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD023592 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami /
Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
History
DepositionApr 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
3: BJ4_G0050160.mRNA.1.CDS.1
2: RNA polymerase II transcription factor B subunit 2
0: General transcription and DNA repair factor IIH helicase subunit XPD
1: Tfb1
4: General transcription and DNA repair factor IIH subunit TFB4
6: General transcription and DNA repair factor IIH
5: General transcription and DNA repair factor IIH subunit TFB5
7: General transcription and DNA repair factor IIH helicase subunit XPB
N: non-template strand DNA
T: template strand DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,27018
Polymers456,46110
Non-polymers8108
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assembly was confirmed by glycerol gradient sedimentation followed by SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules 3216

#1: Protein BJ4_G0050160.mRNA.1.CDS.1 / SX2_G0047880.mRNA.1.CDS.1 / Y55_G0047830.mRNA.1.CDS.1


Mass: 38188.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9BTI9
#2: Protein RNA polymerase II transcription factor B subunit 2


Mass: 58602.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2X3
#4: Protein Tfb1


Mass: 58167.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#6: Protein General transcription and DNA repair factor IIH


Mass: 52024.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9FQL5

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General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 07

#3: Protein General transcription and DNA repair factor IIH helicase subunit XPD / Rad3


Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1C1, DNA helicase
#8: Protein General transcription and DNA repair factor IIH helicase subunit XPB / TFIIH subunit XPB / DNA repair helicase RAD25 / RNA polymerase II transcription factor B subunit ...TFIIH subunit XPB / DNA repair helicase RAD25 / RNA polymerase II transcription factor B subunit SSL2 / TFB subunit SSL2 / Suppressor of stem-loop mutation 2


Mass: 95461.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q00578, DNA helicase

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General transcription and DNA repair factor IIH subunit ... , 2 types, 2 molecules 45

#5: Protein General transcription and DNA repair factor IIH subunit TFB4 / RNA polymerase II transcription factor B subunit 4


Mass: 37430.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9C5C2
#7: Protein General transcription and DNA repair factor IIH subunit TFB5 / TFIIH subunit TFB5 / RNA polymerase II transcription factor B subunit 5


Mass: 8243.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7C1

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DNA chain , 2 types, 2 molecules NT

#9: DNA chain non-template strand DNA


Mass: 9348.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#10: DNA chain template strand DNA


Mass: 9094.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 2 types, 8 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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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: General transcription factor TFIIH (weak binding) / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
12RELION3.1classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101497 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5OQJ

5oqj

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