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- EMDB-8349: Cryo-EM Structure of Yeast Pre-40S, Tsr1 region local class "T2" -

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Basic information

Entry
Database: EMDB / ID: 8349
TitleCryo-EM Structure of Yeast Pre-40S, Tsr1 region local class "T2"
Map dataPre-40S, Tsr1 local class "T2"
Sampleribosomal small subunit late-stage assembly intermediate:
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 10.4 Å resolution
AuthorsJohnson MC / Ghalei H / Doxtader KA / Karbstein K / Stroupe ME
CitationJournal: Structure / Year: 2017
Title: Structural Heterogeneity in Pre-40S Ribosomes.
Authors: Matthew C Johnson / Homa Ghalei / Katelyn A Doxtader / Katrin Karbstein / M Elizabeth Stroupe
Abstract: Late-stage 40S ribosome assembly is a highly regulated dynamic process that occurs in the cytoplasm, alongside the full translation machinery. Seven assembly factors (AFs) regulate and facilitate ...Late-stage 40S ribosome assembly is a highly regulated dynamic process that occurs in the cytoplasm, alongside the full translation machinery. Seven assembly factors (AFs) regulate and facilitate maturation, but the mechanisms through which they work remain undetermined. Here, we present a series of structures of the immature small subunit (pre-40S) determined by three-dimensional (3D) cryoelectron microscopy with 3D sorting to assess the molecule's heterogeneity. These structures demonstrate an extensive structural heterogeneity of interface AFs that likely regulates subunit joining during 40S maturation. We also present structural models for the beak and the platform, two regions where the low resolution of previous studies did not allow for localization of AFs and the rRNA, respectively. These models are supported by biochemical analyses using point variants and suggest that maturation of the 18S 3' end is regulated by dissociation of the AF Dim1 from the subunit interface, consistent with previous biochemical analyses.
DateDeposition: Aug 26, 2016 / Header (metadata) release: Sep 14, 2016 / Map release: Feb 8, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8349.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.62 Å/pix.
= 414.72 Å
256 pix
1.62 Å/pix.
= 414.72 Å
256 pix
1.62 Å/pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-0.12614481 - 0.78471583
Average (Standard dev.)0.004133445 (0.03660998)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 414.72 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720414.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1260.7850.004

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Supplemental data

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Sample components

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Entire ribosomal small subunit late-stage assembly intermediate

EntireName: ribosomal small subunit late-stage assembly intermediate
Number of components: 1

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Component #1: protein, ribosomal small subunit late-stage assembly intermediate

ProteinName: ribosomal small subunit late-stage assembly intermediate
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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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: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 131842
3D reconstructionResolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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