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- EMDB-4088: Monomeric RNA polymerase I at 4.9 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-4088
TitleMonomeric RNA polymerase I at 4.9 A resolution
Map data
SampleS. cerevisiae RNA polymerase I in the monomeric state
  • (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
Function / homology
Function and homology information


termination of RNA polymerase I transcription / transposon integration / nucleolar large rRNA transcription by RNA polymerase I / transcription elongation from RNA polymerase I promoter / RNA polymerase III activity / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE ...termination of RNA polymerase I transcription / transposon integration / nucleolar large rRNA transcription by RNA polymerase I / transcription elongation from RNA polymerase I promoter / RNA polymerase III activity / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II transcribes snRNA genes / mRNA Capping / Formation of the Early Elongation Complex / regulation of cell size / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / promoter-specific chromatin binding / ribonucleoside binding / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / ribosome biogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / DNA-directed RNA polymerase I, subunit RPA34.5 / A49-like RNA polymerase I associated factor / RNA polymerase I associated factor, A49-like / Rpa43, N-terminal ribonucleoprotein (RNP) domain / Pol I subunit A12, C-terminal zinc ribbon / RNA polymerase I, Rpa2 specific domain / DNA-directed RNA polymerase I subunit RPA2, domain 4 ...RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / DNA-directed RNA polymerase I, subunit RPA34.5 / A49-like RNA polymerase I associated factor / RNA polymerase I associated factor, A49-like / Rpa43, N-terminal ribonucleoprotein (RNP) domain / Pol I subunit A12, C-terminal zinc ribbon / RNA polymerase I, Rpa2 specific domain / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / RPA43 OB domain in RNA Pol I / RPA43, OB domain / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb7-like, N-terminal domain superfamily / Zinc finger TFIIS-type signature. / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / RNA polymerase Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / : / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase Rpb5, C-terminal domain / RNA polymerase, subunit H/Rpb5, conserved site / : / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RPB5-like RNA polymerase subunit superfamily / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / C2C2 Zinc finger / Zinc finger TFIIS-type profile. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb6 / : / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 1 / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 3 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerases D / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 6 / DNA-directed RNA polymerase, subunit 2 / RNA polymerases beta chain signature. / RNA polymerase Rpb2, OB-fold
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsTorreira E / Louro JA / Gil-Carton D / Gallego O / Calvo O / Fernandez-Tornero C
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2013-48374-P Spain
Ramon Areces Foundation Spain
CitationJournal: Elife / Year: 2017
Title: The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription.
Authors: Eva Torreira / Jaime Alegrio Louro / Irene Pazos / Noelia González-Polo / David Gil-Carton / Ana Garcia Duran / Sébastien Tosi / Oriol Gallego / Olga Calvo / Carlos Fernández-Tornero /
Abstract: Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental ...Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I-Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association.
History
DepositionOct 11, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseMar 22, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lmx
  • Surface level: 0.14
  • 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_4088.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 162 pix.
= 286.74 Å
1.77 Å/pix.
x 162 pix.
= 286.74 Å
1.77 Å/pix.
x 162 pix.
= 286.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy EMDB: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.18001063 - 0.40812755
Average (Standard dev.)0.0045005027 (±0.024201661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions162162162
Spacing162162162
CellA=B=C: 286.74 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z162162162
origin x/y/z0.0000.0000.000
length x/y/z286.740286.740286.740
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS162162162
D min/max/mean-0.1800.4080.005

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Supplemental data

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Sample components

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Entire S. cerevisiae RNA polymerase I in the monomeric state

EntireName: S. cerevisiae RNA polymerase I in the monomeric state / Number of Components: 16

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Component #1: protein, S. cerevisiae RNA polymerase I in the monomeric state

ProteinName: S. cerevisiae RNA polymerase I in the monomeric state / Recombinant expression: No
MassTheoretical: 594 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,DNA...

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC1,DNA-directed RNA polymerases I and III subunit RPAC1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.850402 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: 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 #6: 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 #7: 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 #8: 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 #9: 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: ligand, ZINC ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.06 mg/mL / pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 95 %

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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: 68 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 47000.0 X (nominal), 79096.0 X (calibrated) / Cs: 2 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1900.0 - 4200.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 1288

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 122348
3D reconstructionSoftware: RELION / Resolution: 4.9 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Overall BValue: 111
Output model

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