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- EMDB-0242: Yeast RNA polymerase I elongation complex bound to nucleotide ana... -

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Basic information

Entry
Database: EMDB / ID: EMD-0242
TitleYeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)
Map dataYeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)
Sample
  • Complex: Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsTafur L / Sadian Y / Weis F / Muller CW
CitationJournal: Elife / Year: 2019
Title: The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2.
Authors: Lucas Tafur / Yashar Sadian / Jonas Hanske / Rene Wetzel / Felix Weis / Christoph W Müller /
Abstract: RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first ...RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first insights into the molecular mechanisms of Pol I transcription. Here, we present cryo-EM structures of yeast Pol I elongation complexes (ECs) bound to the nucleotide analog GMPCPP at 3.2 to 3.4 Å resolution that provide additional insight into the functional interplay between the Pol I-specific transcription-like factors A49-A34.5 and A12.2. Strikingly, most of the nucleotide-bound ECs lack the A49-A34.5 heterodimer and adopt a Pol II-like conformation, in which the A12.2 C-terminal domain is bound in a previously unobserved position at the A135 surface. Our structural and biochemical data suggest a mechanism where reversible binding of the A49-A34.5 heterodimer could contribute to the regulation of Pol I transcription initiation and elongation.
History
DepositionSep 11, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseApr 3, 2019-
UpdateApr 10, 2019-
Current statusApr 10, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00871
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00871
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0242.png

Downloads & links

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Map

FileDownload / File: emd_0242.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 260 pix.
= 270.4 Å		1.04 Å/pix.
x 260 pix.
= 270.4 Å		1.04 Å/pix.
x 260 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00871 / Movie #1: 0.00871
Minimum - Maximum-0.016693646 - 0.04557647
Average (Standard dev.)0.0000065029417 (±0.002637138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 270.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z270.400270.400270.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0170.0460.000

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Supplemental data

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Sample components

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Entire : Yeast RNA polymerase I elongation complex bound to nucleotide ana...

EntireName: Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)
Components
  • Complex: Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)

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Supramolecule #1: Yeast RNA polymerase I elongation complex bound to nucleotide ana...

SupramoleculeName: Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 30 seconds incubation 3 seconds blotting blotting force 3.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5m5x

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 34475
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5m5x

DetailsInitial rigid body fitting was done in Chimera and model building was done in Coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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