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- PDB-8qw9: RNAPII elongation complex bound to RECQ5_R502E -

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Basic information

Entry
Database: PDB / ID: 8qw9
TitleRNAPII elongation complex bound to RECQ5_R502E
Components
  • (DNA, DNA-RNA ELONGATION ...) x 2
  • (DNA-directed RNA polymerase ...) x 6
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • ATP-dependent DNA helicase Q5
  • Polymerase (RNA) II (DNA directed) polypeptide D
  • RNA, DNA-RNA ELONGATION SCAFFOLD
KeywordsTRANSCRIPTION / RNA polymerase II / transcription inhibition / electron cryomicroscopy / electron cryotomography
Function / homology
Function and homology information


Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape ...Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase I Transcription Termination / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Processing of Capped Intron-Containing Pre-mRNA / B-WICH complex positively regulates rRNA expression / mitotic DNA-templated DNA replication / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome separation / cellular response to camptothecin / DNA/RNA hybrid binding / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / negative regulation of transcription elongation by RNA polymerase II / negative regulation of double-strand break repair via homologous recombination / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / core promoter sequence-specific DNA binding / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / DNA helicase activity / replication fork / transcription initiation at RNA polymerase II promoter / P-body / euchromatin / helicase activity / protein-DNA complex / double-strand break repair via homologous recombination / ribonucleoside binding / cellular response to xenobiotic stimulus / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / mitotic cell cycle / single-stranded DNA binding / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / transcription by RNA polymerase II / chromosome, telomeric region / DNA replication / single-stranded RNA binding / protein dimerization activity / hydrolase activity / RNA-directed RNA polymerase / cell division / DNA repair / nucleotide binding / RNA-directed RNA polymerase activity / chromatin binding / nucleolus / magnesium ion binding / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like / 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 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / 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. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / 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 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / Helicase conserved C-terminal domain / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / ATP-dependent DNA helicase Q5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / ATP-dependent DNA helicase Q5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB7
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsSkubnik, K. / Sebesta, M. / Stefl, R.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation Czech Republic
CitationJournal: To Be Published
Title: Spatial organization of RNA polymerase II-RECQ5 transcriptional condensate
Authors: Sebesta, M. / Skubnik, K. / Stefl, R.
History
DepositionOct 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
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
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
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
D: Polymerase (RNA) II (DNA directed) polypeptide D
G: DNA-directed RNA polymerase II subunit RPB7
P: RNA, DNA-RNA ELONGATION SCAFFOLD
T: DNA, DNA-RNA ELONGATION SCAFFOLD
N: DNA, DNA-RNA ELONGATION SCAFFOLD
R: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)628,17924
Polymers627,69716
Non-polymers4828
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area67360 Å2
ΔGint-419 kcal/mol
Surface area161930 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase ... , 6 types, 6 molecules ABCIKG

#1: Protein DNA-directed RNA polymerase subunit


Mass: 217436.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: G3MZY8
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A5PJW8
#3: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 31466.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3T0Q3
#7: Protein DNA-directed RNA polymerase II subunit RPB9


Mass: 14507.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32P73
#9: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II subunit J


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32P79
#12: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q5E9B8

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

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1


Mass: 24514.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2T9T3
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / RPB6 homolog


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32PE0
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F2Z4H3
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32P78
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / DNA-directed RNA polymerase II subunit K


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3ZBC0

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Protein , 2 types, 2 molecules DR

#11: Protein Polymerase (RNA) II (DNA directed) polypeptide D


Mass: 16347.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q1JQ91
#16: Protein ATP-dependent DNA helicase Q5


Mass: 72471.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5 / Production host: Escherichia coli (E. coli) / References: UniProt: O94762

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RNA chain , 1 types, 1 molecules P

#13: RNA chain RNA, DNA-RNA ELONGATION SCAFFOLD


Mass: 5320.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA, DNA-RNA ELONGATION ... , 2 types, 2 molecules TN

#14: DNA chain DNA, DNA-RNA ELONGATION SCAFFOLD


Mass: 15780.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA, DNA-RNA ELONGATION SCAFFOLD


Mass: 16861.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 8 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1RNAP II EC -- RECQ5_R502E(1-650)COMPLEX#1-#160MULTIPLE SOURCES
2DNA-directed RNA polymeraseCOMPLEX#1-#121NATURAL
3DNA-RNA ELONGATION SCAFFOLDCOMPLEX#13-#151RECOMBINANT
4ATP-dependent DNA helicase Q5COMPLEX#151RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Bos taurus (domestic cattle)9913
33synthetic construct (others)32630
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13synthetic construct (others)32630
24Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 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: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9046

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 787289
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19142 / Num. of class averages: 1 / Symmetry type: POINT

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