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- EMDB-4429: Structure of transcribing RNA polymerase II-nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4429
TitleStructure of transcribing RNA polymerase II-nucleosome complex
Map data
SampleComplex of S. cerevisiae RNA polymerase II and X. leaves NCP
  • Histone H3.2
  • Histone H2A type 1
  • (nucleic-acidNucleic acid) x 3
  • Histone H4
  • Histone H2B 1.1
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (ligand) x 2
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase III transcription / positive regulation of translational initiation / RNA polymerase I activity ...nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase III transcription / positive regulation of translational initiation / RNA polymerase I activity / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / mRNA cleavage / RNA polymerase II, core complex / transcription by RNA polymerase I / transcription by RNA polymerase III / transcription, RNA-templated / termination of RNA polymerase II transcription / translation initiation factor binding / ribonucleoside binding / single-stranded RNA binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription, initiation / P-body / nucleosome / ribosome biogenesis / transcription-coupled nucleotide-excision repair / cytoplasmic stress granule / single-stranded DNA binding / translesion synthesis / transcription by RNA polymerase II / transcription initiation from RNA polymerase II promoter / nucleic acid binding / protein dimerization activity / mRNA binding / cellular response to DNA damage stimulus / nucleolus / nucleotide binding / protein heterodimerization activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerases, subunit N, zinc binding site / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit ...RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerases, subunit N, zinc binding site / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb1, domain 4 / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / TATA box binding protein associated factor (TAF) / S1 domain / Histone H2A / Histone H4 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, insert domain / RNA polymerase, subunit H/Rpb5, conserved site / Histone H4, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Nucleic acid-binding, OB-fold / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / HRDC-like superfamily / RNA polymerase, beta subunit, conserved site / Histone-fold / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / Histone H2A/H2B/H3 / RNA polymerase, alpha subunit / Histone H2B / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb1, domain 3 superfamily / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase Rpb1, domain 7 superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase RBP11 / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerase, subunit N/Rpb10 / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / CENP-T/Histone H4, histone fold / Histone H2A, C-terminal domain / Histone H3/CENP-A / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / Pol II subunit B9, C-terminal zinc ribbon / Histone H2A conserved site
DNA-directed RNA polymerases I, II, and III subunit RPABC3 / Histone H4 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...DNA-directed RNA polymerases I, II, and III subunit RPABC3 / Histone H4 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / Histone H2A type 1 / DNA-directed RNA polymerase II subunit RPB1 / Histone H2B 1.1 / Histone H3.2
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsFarnung L / Vos SM / Cramer P
Funding support Germany, 4 items
OrganizationGrant numberCountry
European Research CouncilTransregulon (693023) Germany
German Research FoundationSFB1064 Germany
European Molecular Biology OrganizationALTF-725-2014 Germany
German Research FoundationSFB860 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structure of transcribing RNA polymerase II-nucleosome complex.
Authors: Lucas Farnung / Seychelle M Vos / Patrick Cramer /
Abstract: Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of ...Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription.
Validation ReportPDB-ID: 6i84

SummaryFull reportAbout validation report
History
DepositionNov 19, 2018-
Header (metadata) releaseJan 2, 2019-
Map releaseJan 2, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0173
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0173
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6i84
  • Surface level: 0.0173
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4429.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å
1.05 Å/pix.
x 320 pix.
= 336. Å
1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0173 / Movie #1: 0.0173
Minimum - Maximum-0.040229578 - 0.09701496
Average (Standard dev.)0.000027996 (±0.004242378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0070.048-0.000

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Supplemental data

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: emd 4429.png

Fileemd_4429.png
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Complex of S. cerevisiae RNA polymerase II and X. leaves NCP

EntireName: Complex of S. cerevisiae RNA polymerase II and X. leaves NCP
Number of components: 25

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Component #1: protein, Complex of S. cerevisiae RNA polymerase II and X. leaves NCP

ProteinName: Complex of S. cerevisiae RNA polymerase II and X. leaves NCP
Recombinant expression: No

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Component #2: protein, Complex of S. cerevisiae RNA polymerase II and X. leaves NCP

ProteinName: Complex of S. cerevisiae RNA polymerase II and X. leaves NCP
Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Complex of S. cerevisiae RNA polymerase II and X. leaves NCP

ProteinName: Complex of S. cerevisiae RNA polymerase II and X. leaves NCP
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #4: protein, Complex of S. cerevisiae RNA polymerase II and X. leaves NCP

ProteinName: Complex of S. cerevisiae RNA polymerase II and X. leaves NCP
Recombinant expression: No
SourceSpecies: synthetic construct (others)

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Component #5: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.435126 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.109436 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: nucleic-acid, DNA (170-MER)

nucleic acidName: DNA (170-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC)(DA)(DG)(DC)(DT)(DC) ...Sequence:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC) (DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA) (DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC) (DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG)(DA)(DT)(DA)(DT)(DA)(DG)(DG) (DA)(DA)(DT)(DA)(DA)(DC)(DA)(DG)(DG)(DA) (DT)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DG)
MassTheoretical: 52.041215 kDa
SourceSpecies: synthetic construct (others)

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Component #8: nucleic-acid, DNA (158-MER)

nucleic acidName: DNA (158-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DC)(DC)(DT)(DG)(DT)(DT)(DA)(DT)(DT) (DC)(DC)(DT)(DA)(DT)(DA)(DT)(DC)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG) ...Sequence:
(DT)(DC)(DC)(DT)(DG)(DT)(DT)(DA)(DT)(DT) (DC)(DC)(DT)(DA)(DT)(DA)(DT)(DC)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC) (DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT)
MassTheoretical: 49.537551 kDa
SourceSpecies: synthetic construct (others)

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Component #9: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.655948 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 191.821578 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #12: protein, DNA-directed RNA polymerase II subunit RPB2

ProteinName: DNA-directed RNA polymerase II subunit RPB2Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 138.937297 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #13: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.809113 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #14: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.451191 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #15: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #16: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #17: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.081053 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #18: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #19: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.308161 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #20: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #21: protein, DNA-directed RNA polymerase II subunit RPB11

ProteinName: DNA-directed RNA polymerase II subunit RPB11Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.633493 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #22: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #23: nucleic-acid, RNA

nucleic acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCUCACUGGA
MassTheoretical: 3.137908 kDa
SourceSpecies: synthetic construct (others)

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Component #24: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #25: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 46 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 49703
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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