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- PDB-9pb7: TFIIH of PIC-Med-SWI/SNF -

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Basic information

Entry
Database: PDB / ID: 9pb7
TitleTFIIH of PIC-Med-SWI/SNF
Components
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription and DNA repair factor IIH subunit ...) x 5
  • (promoter DNA) x 2
  • RNA polymerase II transcription factor B subunit 3
  • SWI/SNF chromatin-remodeling complex subunit SNF5
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION/DNA / SWI/SNF / PIC / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


carbon catabolite activation of transcription / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / positive regulation of invasive growth in response to glucose limitation / regulation of mitotic recombination / transcription open complex formation at RNA polymerase II promoter / phosphatidylinositol-5-phosphate binding / RNA polymerase II promoter clearance / positive regulation of mitotic recombination ...carbon catabolite activation of transcription / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / positive regulation of invasive growth in response to glucose limitation / regulation of mitotic recombination / transcription open complex formation at RNA polymerase II promoter / phosphatidylinositol-5-phosphate binding / RNA polymerase II promoter clearance / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIK complex / transcription factor TFIIF complex / phosphatidylinositol-3-phosphate binding / mediator complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Ino80 complex / cyclin-dependent protein serine/threonine kinase activator activity / SWI/SNF complex / DNA 5'-3' helicase / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / nuclear chromosome / RNA Polymerase II Pre-transcription Events / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA 3'-5' helicase / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / 3'-5' DNA helicase activity / RNA polymerase II preinitiation complex assembly / transcription by RNA polymerase I / DNA helicase activity / transcription initiation at RNA polymerase II promoter / double-strand break repair via homologous recombination / nucleotide-excision repair / transcription by RNA polymerase II / 4 iron, 4 sulfur cluster binding / ubiquitin protein ligase activity / double-stranded DNA binding / histone binding / 5'-3' DNA helicase activity / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / DNA repair / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA-templated transcription / DNA binding / zinc ion binding / ATP binding / nucleus / cytosol
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Bacterial type XPD DNA helicase, FeS cluster domain / : / YEATS superfamily / YEATS family / YEATS domain profile. / TFIIH subunit Tfb4/GTF2H3 ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Bacterial type XPD DNA helicase, FeS cluster domain / : / YEATS superfamily / YEATS family / YEATS domain profile. / 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 / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ERCC3/RAD25/XPB helicase, C-terminal domain / : / ATP-dependent helicase Rad3/Chl1-like / 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-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / 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. / C1-like domain superfamily / NET domain / Bromodomain extra-terminal - transcription regulation / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / PH-like domain superfamily / 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/RAD3 / SWI/SNF chromatin-remodeling complex subunit SNF5 / General transcription and DNA repair factor IIH subunit TFB1 / Transcription initiation factor TFIID subunit 14 / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB2 / RNA polymerase II transcription factor B subunit 3 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / SWI/SNF chromatin-remodeling complex subunit SNF5 / General transcription and DNA repair factor IIH subunit TFB1 / Transcription initiation factor TFIID subunit 14 / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB2 / RNA polymerase II transcription factor B subunit 3 / General transcription and DNA repair factor IIH subunit SSL1 / General transcription and DNA repair factor IIH subunit TFB4 / 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: 4.4 Å
AuthorsYang, C. / Nagai, S. / Chen, D.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure of TFIIH of PIC-Med-SWI/SNF
Authors: Yang, C. / Nagai, S. / Chen, D.-H.
History
DepositionJun 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
5: General transcription and DNA repair factor IIH subunit TFB5
0: General transcription and DNA repair factor IIH helicase subunit XPD/RAD3
3: RNA polymerase II transcription factor B subunit 3
7: General transcription and DNA repair factor IIH helicase subunit XPB
8: SWI/SNF chromatin-remodeling complex subunit SNF5
9: Transcription initiation factor TFIID subunit 14
N: promoter DNA
T: promoter DNA
4: General transcription and DNA repair factor IIH subunit TFB4
6: General transcription and DNA repair factor IIH subunit SSL1
1: General transcription and DNA repair factor IIH subunit TFB1
2: General transcription and DNA repair factor IIH subunit TFB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)600,16020
Polymers599,35012
Non-polymers8108
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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General transcription and DNA repair factor IIH subunit ... , 5 types, 5 molecules 54612

#1: 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
#9: Protein General transcription and DNA repair factor IIH subunit TFB4 / TFIIH subunit TFB4 / RNA polymerase II transcription factor B 34 kDa subunit / RNA polymerase II ...TFIIH subunit TFB4 / RNA polymerase II transcription factor B 34 kDa subunit / RNA polymerase II transcription factor B p34 subunit / RNA polymerase II transcription factor B subunit 4


Mass: 37506.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12004
#10: Protein General transcription and DNA repair factor IIH subunit SSL1 / TFIIH subunit SSL1 / RNA polymerase II transcription factor B subunit SSL1 / TFB subunit SSL1 / ...TFIIH subunit SSL1 / RNA polymerase II transcription factor B subunit SSL1 / TFB subunit SSL1 / Suppressor of stem-loop protein 1


Mass: 52370.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04673
#11: Protein General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II ...TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit / RNA polymerase II transcription factor B subunit 1


Mass: 72993.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32776
#12: Protein General transcription and DNA repair factor IIH subunit TFB2 / TFIIH subunit TFB2 / RNA polymerase II transcription factor B 52 kDa subunit / RNA polymerase II ...TFIIH subunit TFB2 / RNA polymerase II transcription factor B 52 kDa subunit / RNA polymerase II transcription factor B p52 subunit / 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: Q02939

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

#2: Protein General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / TFIIH subunit XPD / DNA 5'-3' helicase RAD3 / DNA repair helicase RAD3 / RNA polymerase II ...TFIIH subunit XPD / DNA 5'-3' helicase RAD3 / DNA repair helicase RAD3 / RNA polymerase II transcription factor B subunit RAD3 / TFB subunit 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: P06839, DNA 5'-3' helicase
#4: 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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Protein , 3 types, 3 molecules 389

#3: Protein RNA polymerase II transcription factor B subunit 3 / RNA polymerase II transcription factor B 38 kDa subunit / RNA polymerase II transcription factor B p38 subunit


Mass: 38188.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03290
#5: Protein SWI/SNF chromatin-remodeling complex subunit SNF5 / SWI/SNF complex subunit SNF5 / Transcription factor TYE4 / Transcription regulatory protein SNF5


Mass: 102642.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P18480
#6: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 27473.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35189

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DNA chain , 2 types, 2 molecules NT

#7: DNA chain promoter DNA


Mass: 8007.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#8: DNA chain promoter DNA


Mass: 7963.193 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

#13: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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: TFIIH of PIC-Med-SWI/SNF / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Details: 40 mM Hepes-KOH pH 7.5 100 mM potassium acetate 2 mM magnesium acetate 5 mM DTT
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.20.1_4487model refinement
3SerialEMimage acquisition
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 433107 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01427124
ELECTRON MICROSCOPYf_angle_d1.75636872
ELECTRON MICROSCOPYf_dihedral_angle_d15.3353933
ELECTRON MICROSCOPYf_chiral_restr0.094207
ELECTRON MICROSCOPYf_plane_restr0.0124515

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