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- EMDB-0219: Cryo-EM structure 2 of pre-60S particles isolated via Arx1-FTpA f... -

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Basic information

Entry
Database: EMDB / ID: EMD-0219
TitleCryo-EM structure 2 of pre-60S particles isolated via Arx1-FTpA from yeast
Map data
Sample
  • Complex: Yeast pre60S particle purified via Arx1-FTpA
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsKater L / Beckmann R
CitationJournal: Nat Commun / Year: 2018
Title: Suppressor mutations in Rpf2-Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation.
Authors: Matthias Thoms / Valentin Mitterer / Lukas Kater / Laurent Falquet / Roland Beckmann / Dieter Kressler / Ed Hurt /
Abstract: During eukaryotic 60S biogenesis, the 5S RNP requires a large rotational movement to achieve its mature position. Cryo-EM of the Rix1-Rea1 pre-60S particle has revealed the post-rotation stage, in ...During eukaryotic 60S biogenesis, the 5S RNP requires a large rotational movement to achieve its mature position. Cryo-EM of the Rix1-Rea1 pre-60S particle has revealed the post-rotation stage, in which a gently undulating α-helix corresponding to Cgr1 becomes wedged between Rsa4 and the relocated 5S RNP, but the purpose of this insertion was unknown. Here, we show that cgr1 deletion in yeast causes a slow-growth phenotype and reversion of the pre-60S particle to the pre-rotation stage. However, spontaneous extragenic suppressors could be isolated, which restore growth and pre-60S biogenesis in the absence of Cgr1. Whole-genome sequencing reveals that the suppressor mutations map in the Rpf2-Rrs1 module and Rpl5, which together stabilize the unrotated stage of the 5S RNP. Thus, mutations in factors stabilizing the pre-rotation stage facilitate 5S RNP relocation upon deletion of Cgr1, but Cgr1 itself could stabilize the post-rotation stage.
History
DepositionAug 29, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateOct 17, 2018-
Current statusOct 17, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0219.png

Downloads & links

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Map

FileDownload / File: emd_0219.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.55 Å/pix.
x 140 pix.
= 357. Å		2.55 Å/pix.
x 140 pix.
= 357. Å		2.55 Å/pix.
x 140 pix.
= 357. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.55 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.027233819 - 0.115509644
Average (Standard dev.)0.0037600768 (±0.018886808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 357.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.552.552.55
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z357.000357.000357.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.0270.1160.004

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Supplemental data

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Sample components

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Entire : Yeast pre60S particle purified via Arx1-FTpA

EntireName: Yeast pre60S particle purified via Arx1-FTpA
Components
  • Complex: Yeast pre60S particle purified via Arx1-FTpA

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Supramolecule #1: Yeast pre60S particle purified via Arx1-FTpA

SupramoleculeName: Yeast pre60S particle purified via Arx1-FTpA / type: complex / ID: 1 / Parent: 0
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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F216 (2k x 2k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

3199

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 10380
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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