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- PDB-9pbd: PolII/TFIIF of PIC-Med-SWI/SNF -

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Entry
Database: PDB / ID: 9pbd
TitlePolII/TFIIF of PIC-Med-SWI/SNF
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Transcription ...) x 4
KeywordsTRANSCRIPTION / SWI/SNF / PIC
Function / homology
Function and homology information


transcription open complex formation at RNA polymerase II promoter / regulation of mRNA 3'-end processing / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RPB4-RPB7 complex / transcription elongation factor activity / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation ...transcription open complex formation at RNA polymerase II promoter / regulation of mRNA 3'-end processing / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RPB4-RPB7 complex / transcription elongation factor activity / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / 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 / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / RNA polymerase II transcribes snRNA genes / 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 / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / termination of RNA polymerase II transcription / protein phosphatase activator activity / termination of RNA polymerase I transcription / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase III / nuclear-transcribed mRNA catabolic process / RNA polymerase II preinitiation complex assembly / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / proteasome storage granule / transcription-coupled nucleotide-excision repair / translesion synthesis / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription elongation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription antitermination / positive regulation of transcription elongation by RNA polymerase II / DNA-templated transcription initiation / P-body / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / single-stranded DNA binding / nucleic acid binding / transcription coactivator activity / protein dimerization activity / single-stranded RNA binding / nucleotide binding / mRNA binding / nucleolus / regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain superfamily / Transcription elongation factor S-II, central domain / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. ...Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain superfamily / Transcription elongation factor S-II, central domain / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TFIIS/LEDGF domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / Cyclin-like superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / Zinc finger, TFIIS-type / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 ...DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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 PolII/TFIIF of PIC-Med-SWI/SNF
Authors: Yang, C. / Nagai, S. / Chen, D.-H.
History
DepositionJun 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 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
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
S: Transcription elongation factor S-II
Q: Transcription initiation factor IIF subunit alpha
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
D: DNA-directed RNA polymerase II subunit RPB4
R: Transcription initiation factor IIF subunit beta
M: Transcription initiation factor IIB
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)717,00327
Polymers716,32416
Non-polymers67811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules CGIKABD

#1: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II ...RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370
#4: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087
#5: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999
#7: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902
#11: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFJLH

#2: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#3: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422
#16: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436

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Transcription ... , 4 types, 4 molecules SQRM

#9: Protein Transcription elongation factor S-II / DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway ...DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway regulatory protein 2


Mass: 34903.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DST1, PPR2, YGL043W / Production host: Escherichia coli (E. coli) / References: UniProt: P07273
#10: Protein Transcription initiation factor IIF subunit alpha / TFIIF-alpha / TFIIF large subunit / Transcription factor G 105 kDa subunit / P105


Mass: 82320.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41895
#14: Protein Transcription initiation factor IIF subunit beta / TFIIF medium subunit / TFIIF-beta / Transcription factor G 54 kDa subunit


Mass: 46684.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41896
#15: Protein Transcription initiation factor IIB / General transcription factor TFIIB / Transcription factor E


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUA7, YPR086W, P9513.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P29055

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Non-polymers , 2 types, 11 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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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: PolII/TFIIF of PIC-Med-SWI/SNF / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
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 and 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 magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / 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)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.20.1_4487model refinement
3SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2985639 / 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_d0.01237317
ELECTRON MICROSCOPYf_angle_d1.63350339
ELECTRON MICROSCOPYf_dihedral_angle_d6.5865002
ELECTRON MICROSCOPYf_chiral_restr0.1045629
ELECTRON MICROSCOPYf_plane_restr0.0146529

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