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- EMDB-4086: RNA polymerase I-Rrn3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4086
TitleRNA polymerase I-Rrn3 complex
Map dataPol I-Rrn3 complex
Sample
  • Complex: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsTorreira E / Louro JA / Gil-Carton D / Gallego O / Calvo O / Fernandez-Tornero C
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
DepositionAug 2, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseMar 22, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4086.png

Downloads & links

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Map

FileDownload / File: emd_4086.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPol I-Rrn3 complex
Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.09232628 - 0.28997466
Average (Standard dev.)0.00456031 (±0.023206301)
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-0.0920.2900.005

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Supplemental data

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Sample components

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Entire : S. cerevisiae RNA polymerase I in complex with activating factor Rrn3

EntireName: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3
Components
  • Complex: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3

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Supramolecule #1: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3

SupramoleculeName: S. cerevisiae RNA polymerase I in complex with activating factor Rrn3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 594 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.06 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMNaClSodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-68 / Number grids imaged: 1 / Number real images: 1288 / Average exposure time: 4.0 sec. / Average electron dose: 68.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 190750
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: OTHER
Details: Negative-staining reconstruction of RNA polymerase I
Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 6 / Avg.num./class: 30000 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 32175
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 537

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