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- EMDB-4147: Yeast RNA polymerase I elongation complex at 3.8A -

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Entry
Database: EMDB / ID: 4147
TitleYeast RNA polymerase I elongation complex at 3.8A
Map dataSharpened map (B=-149A^2)
SampleYeast RNA polymerase I elongation complex
  • (DNA-directed RNA polymerase I subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (nucleic-acidNucleic acid) x 3
  • (ligand) x 3
Function / homologyDNA-directed RNA polymerases I and III subunit AC19 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily ...DNA-directed RNA polymerases I and III subunit AC19 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / 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 / RNA polymerase, RBP11-like subunit / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb3/Rpb11 dimerisation domain / Pol I subunit A12, C-terminal zinc ribbon / DNA-directed RNA polymerases I and III subunit AC40 / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase Rpb6 / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Yeast RNA polymerase I subunit RPA14 / RNA Polymerase II Pre-transcription Events / Formation of the Early Elongation Complex / Zinc finger TFIIS-type profile. / RNA polymerases beta chain signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases M / 15 Kd subunits signature. / Zinc finger TFIIS-type signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, Rpa2 specific domain / RNA polymerases M/15 Kd subunit / A49-like RNA polymerase I associated factor / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase I, subunit RPA34.5 / Dual incision in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase I, subunit Rpa14, fungi / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase II transcribes snRNA genes / RNA polymerase, subunit omega/K/RPB6 / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / 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 Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA polymerase Rpb7, N-terminal / RNA polymerase, subunit H/Rpb5 C-terminal / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, beta subunit, protrusion / 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 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase I subunit RPA2, domain 4 / RNA polymerase I associated factor, A49-like / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 3 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Formation of TC-NER Pre-Incision Complex
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsNeyer S / Kunz M / Geiss C / Hantsche M / Hodirnau V-V / Seybert A / Engel C / Scheffer MP / Cramer P / Frangakis AS
CitationJournal: Nature / Year: 2016
Title: Structure of RNA polymerase I transcribing ribosomal DNA genes.
Authors: Simon Neyer / Michael Kunz / Christian Geiss / Merle Hantsche / Victor-Valentin Hodirnau / Anja Seybert / Christoph Engel / Margot P Scheffer / Patrick Cramer / Achilleas S Frangakis
Validation ReportPDB-ID: 5m3f

SummaryFull reportAbout validation report
DateDeposition: Oct 14, 2016 / Header (metadata) release: Nov 23, 2016 / Map release: Nov 23, 2016 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5m3f
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4147.map.gz (map file in CCP4 format, 48669 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
230 pix
1.05 Å/pix.
= 241.5 Å
230 pix
1.05 Å/pix.
= 241.5 Å
230 pix
1.05 Å/pix.
= 241.5 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 Level:0.045 (by author), 0.04 (movie #1):
Minimum - Maximum-0.14176147 - 0.21848649
Average (Standard dev.)-0.000036260455 (0.009844061)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions230230230
Origin0.00.00.0
Limit229.0229.0229.0
Spacing230230230
CellA=B=C: 241.49998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z241.500241.500241.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.1420.218-0.000

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Supplemental data

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Sample components

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Entire Yeast RNA polymerase I elongation complex

EntireName: Yeast RNA polymerase I elongation complex / Number of components: 21

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Component #1: protein, Yeast RNA polymerase I elongation complex

ProteinName: Yeast RNA polymerase I elongation complex / Recombinant expression: No
MassTheoretical: 590 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, DNA-directed RNA polymerase I subunit RPA190

ProteinName: DNA-directed RNA polymerase I subunit RPA190Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 186.676969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #3: protein, DNA-directed RNA polymerase I subunit RPA135

ProteinName: DNA-directed RNA polymerase I subunit RPA135Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 135.910328 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #4: protein, DNA-directed RNA polymerases I and III subunit RPAC1

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.732613 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #5: 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: Baker's yeast (baker's yeast) / Strain: S288c

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Component #6: 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: Baker's yeast (baker's yeast) / Strain: S288c

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Component #7: 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: Baker's yeast (baker's yeast) / Strain: S288c

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Component #8: protein, DNA-directed RNA polymerase I subunit RPA12

ProteinName: DNA-directed RNA polymerase I subunit RPA12Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.676566 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #9: 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: Baker's yeast (baker's yeast) / Strain: S288c

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Component #10: protein, DNA-directed RNA polymerases I and III subunit RPAC2

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.16786 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #11: 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: Baker's yeast (baker's yeast) / Strain: S288c

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Component #12: nucleic-acid, template DNA

Nucleic-acidName: template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT) (DA)(DC)(DT)(DT)(DA)(DA)(DG)(DC)(DC)(DT) (DG)(DG)(DT)(DC)(DA)(DT)(DT)(DA)(DC)(DT) (DA)(DG)(DT)(DA)(DC)(DT)(DG)(DC)(DC)
MassTheoretical: 11.942696 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #13: nucleic-acid, non-template DNA

Nucleic-acidName: non-template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DA) (DG)(DT)(DA)(DA)(DA)(DC)(DT)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DA)(DG)(DT)(DA) (DC)(DT)(DT)(DG)(DA)(DG)(DC)(DT)(DT)
MassTheoretical: 12.085806 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #14: nucleic-acid, RNA

Nucleic-acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUCUGCAUG UAGACCAGGC
MassTheoretical: 6.383838 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #15: protein, DNA-directed RNA polymerase I subunit RPA49

ProteinName: DNA-directed RNA polymerase I subunit RPA49Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.721707 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #16: protein, DNA-directed RNA polymerase I subunit RPA34

ProteinName: DNA-directed RNA polymerase I subunit RPA34Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.933518 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #17: protein, DNA-directed RNA polymerase I subunit RPA14

ProteinName: DNA-directed RNA polymerase I subunit RPA14Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.599128 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #18: protein, DNA-directed RNA polymerase I subunit RPA43

ProteinName: DNA-directed RNA polymerase I subunit RPA43Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.264852 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #19: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #20: ligand, MAGNESIUM ION

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

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Component #21: ligand, SULFATE ION

LigandName: SULFATE IONSulfate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.606305 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: blot force 13, blotting time 8.5s.

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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: 56 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 94000
3D reconstructionResolution: 3.8 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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