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- EMDB-4148: Free monomeric RNA polymerase I at 4.0A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-4148
TitleFree monomeric RNA polymerase I at 4.0A resolution
Map data
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
  • (ligand) x 2
Function / homology
Function and homology information


RNA polymerase I preinitiation complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / termination of RNA polymerase III transcription / RNA polymerase I activity / regulation of cell size / tRNA transcription by RNA polymerase III ...RNA polymerase I preinitiation complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / termination of RNA polymerase III transcription / RNA polymerase I activity / regulation of cell size / 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 / ribonucleoside binding / DNA-directed RNA polymerase / promoter-specific chromatin binding / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / host cell nucleus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, conserved site / RNA polymerase I associated factor, A49-like / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain ...RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, conserved site / RNA polymerase I associated factor, A49-like / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, insert domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb7-like , N-terminal / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerases I and III subunit AC19 / 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 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase I, subunit RPA34.5 / RNA polymerase I, subunit Rpa14, fungi / Nucleic acid-binding, OB-fold / RNA polymerase subunit, RPB6/omega / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase, Rpb5, N-terminal / Pol I subunit A12, C-terminal zinc ribbon / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb1, domain 3 superfamily / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RPA43, OB domain / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerases I and III subunit AC40 / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase, subunit N/Rpb10 / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily
DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerase I subunit RPA49
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
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 /
Abstract: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces ...RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.
Validation ReportPDB-ID: 5m3m

SummaryFull reportAbout validation report
History
DepositionOct 15, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseNov 23, 2016-
UpdateFeb 20, 2019-
Current statusFeb 20, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5m3m
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4148.map.gz / Format: CCP4 / Size: 46.4 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 230 pix.
= 241.5 Å
1.05 Å/pix.
x 230 pix.
= 241.5 Å
1.05 Å/pix.
x 230 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 LevelBy AUTHOR: 0.04 / Movie #1: 0.03
Minimum - Maximum-0.09353096 - 0.15214713
Average (Standard dev.)-0.000035655336 (±0.0072155506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 241.49998 Å
α=β=γ: 90.0 °

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-0.0940.152-0.000

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Supplemental data

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Additional map: Map filtered to 4.2A

Fileemd_4148_additional.map
AnnotationMap filtered to 4.2A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map1

Fileemd_4148_half_map_1.map
AnnotationUnfiltered half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map2

Fileemd_4148_half_map_2.map
AnnotationUnfiltered half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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: 17

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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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / 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: ATCC 204508 / S288c

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Component #12: 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: ATCC 204508 / S288c

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Component #13: 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: ATCC 204508 / S288c

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Component #14: 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: ATCC 204508 / S288c

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Component #15: 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: ATCC 204508 / S288c

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Component #16: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #17: 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 reconstructionSoftware: RELION / Resolution: 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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