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- EMDB-30112: Cryo-EM structure of pre-60S ribosomal subunit from Saccharomyces... -

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Basic information

Entry
Database: EMDB / ID: EMD-30112
TitleCryo-EM structure of pre-60S ribosomal subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C3 state at 3.9 Angstroms resolution.
Map dataCryo-EM structure of pre-60S ribosomal subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C3 state at 3.9 Angstroms resolution.
Sample
  • Complex: Eukaryotic pre-60S ribosomal subunits
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLi Y / Micic J
Funding support China, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM028301 China
Ministry of Science and Technology (MoST, China)2016YFA0500700 China
National Natural Science Foundation of China (NSFC)31725007; 31630087 China
CitationJournal: Nat Commun / Year: 2020
Title: Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly.
Authors: Jelena Micic / Yu Li / Shan Wu / Daniel Wilson / Beril Tutuncuoglu / Ning Gao / John L Woolford /
Abstract: The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring ...The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring of the Rpf2 subcomplex containing 5S rRNA, rpL5, rpL11, Rpf2 and Rrs1, which initially docks onto the flexible domain V of rRNA at earlier stages of assembly. In this work, we tested the function of the C-terminal domain (CTD) of Rpf2 during these anchoring steps, by truncating this extension and assaying effects on middle stages of subunit maturation. The rpf2Δ255-344 mutation affects proper folding of rRNA helices H68-70 during anchoring of the Rpf2 subcomplex. In addition, several assembly factors (AFs) are absent from pre-ribosomes or in altered conformations. Consequently, major remodeling events fail to occur: rotation of the 5S RNP, maturation of the peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), and export of assembling subunits to the cytoplasm.
History
DepositionMar 13, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30112.png

Downloads & links

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Map

FileDownload / File: emd_30112.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of pre-60S ribosomal subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C3 state at 3.9 Angstroms resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 422.8 Å		1.06 Å/pix.
x 400 pix.
= 422.8 Å		1.06 Å/pix.
x 400 pix.
= 422.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.009207286 - 0.041603625
Average (Standard dev.)0.0008193033 (±0.0031253234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 422.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0571.0571.057
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z422.800422.800422.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0090.0420.001

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Supplemental data

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Sample components

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Entire : Eukaryotic pre-60S ribosomal subunits

EntireName: Eukaryotic pre-60S ribosomal subunits
Components
  • Complex: Eukaryotic pre-60S ribosomal subunits

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Supramolecule #1: Eukaryotic pre-60S ribosomal subunits

SupramoleculeName: Eukaryotic pre-60S ribosomal subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#58
Source (natural)Organism: Saccharomyces cerevisiae S288C (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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 335820
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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