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- EMDB-6697: Cryo-EM structure of the 90S small subunit pre-ribosome (Noc4-TAP) -

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Database: EMDB / ID: EMD-6697
TitleCryo-EM structure of the 90S small subunit pre-ribosome (Noc4-TAP)
Map data
Sample90S small subunit pre-ribosome (Noc4-TAP)
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsYe K / Zhu X / Sun Q
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
DepositionJan 16, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseMar 29, 2017-
UpdateMar 29, 2017-
Current statusMar 29, 2017Processing site: PDBj / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_6697.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 480 pix.
= 681.6 Å
1.42 Å/pix.
x 480 pix.
= 681.6 Å
1.42 Å/pix.
x 480 pix.
= 681.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.05033438 - 0.12918253
Average (Standard dev.)0.00035046774 (±0.0073576695)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 681.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z681.600681.600681.600
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0500.1290.000

Supplemental data

Sample components

Entire 90S small subunit pre-ribosome (Noc4-TAP)

EntireName: 90S small subunit pre-ribosome (Noc4-TAP) / Number of components: 1

Component #1: protein, 90S small subunit pre-ribosome (Noc4-TAP)

ProteinName: 90S small subunit pre-ribosome (Noc4-TAP) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 52000.0 X (nominal), 98592.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 5000.0 nm
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1769

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 12643
3D reconstructionSoftware: Relion / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: use the default parameters of Relion
FSC plot (resolution estimation)

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