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- EMDB-4096: Cryo-EM structure of the Yvh1 pre-60S particle -

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Basic information

Entry
Database: EMDB / ID: EMD-4096
TitleCryo-EM structure of the Yvh1 pre-60S particle
Map dataYvh1 pre-60S particle
Sample
  • Complex: Yvh1 pre-60S particle
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsSarkar A / Pech M / Thoms M / Beckmann R / Hurt E
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Ribosome-stalk biogenesis is coupled with recruitment of nuclear-export factor to the nascent 60S subunit.
Authors: Anshuk Sarkar / Markus Pech / Matthias Thoms / Roland Beckmann / Ed Hurt /
Abstract: Nuclear export of preribosomal subunits is a key step during eukaryotic ribosome formation. To efficiently pass through the FG-repeat meshwork of the nuclear pore complex, the large pre-60S subunit ...Nuclear export of preribosomal subunits is a key step during eukaryotic ribosome formation. To efficiently pass through the FG-repeat meshwork of the nuclear pore complex, the large pre-60S subunit requires several export factors. Here we describe the mechanism of recruitment of the Saccharomyces cerevisiae RNA-export receptor Mex67-Mtr2 to the pre-60S subunit at the proper time. Mex67-Mtr2 binds at the premature ribosomal-stalk region, which later during translation serves as a binding platform for translational GTPases on the mature ribosome. The assembly factor Mrt4, a structural homolog of cytoplasmic-stalk protein P0, masks this site, thus preventing untimely recruitment of Mex67-Mtr2 to nuclear pre-60S particles. Subsequently, Yvh1 triggers Mrt4 release in the nucleus, thereby creating a narrow time window for Mex67-Mtr2 association at this site and facilitating nuclear export of the large subunit. Thus, a spatiotemporal mark on the ribosomal stalk controls the recruitment of an RNA-export receptor to the nascent 60S subunit.
History
DepositionAug 8, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseOct 12, 2016-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4096.png

Downloads & links

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Map

FileDownload / File: emd_4096.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYvh1 pre-60S particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 446.04 Å		1.06 Å/pix.
x 420 pix.
= 446.04 Å		1.06 Å/pix.
x 420 pix.
= 446.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-3.8348014 - 9.691725999999999
Average (Standard dev.)-0.002149311 (±0.6055831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 446.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z446.040446.040446.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-3.8359.692-0.002

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Supplemental data

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Sample components

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Entire : Yvh1 pre-60S particle

EntireName: Yvh1 pre-60S particle
Components
  • Complex: Yvh1 pre-60S particle

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Supramolecule #1: Yvh1 pre-60S particle

SupramoleculeName: Yvh1 pre-60S particle / 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

Concentration2.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
50.0 mMTris-HCl
100.0 mMNaCl
5.0 mMMgCl2
1.0 mMDTT
0.075 %NP40
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Details: Method Blot for 3 seconds before plunging.
DetailsThe freshly prepared pre-60S sample was applied to 2 nm pre-coated Quantifoil holey carbon supparted grids an vitrified

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number real images: 3226 / Average electron dose: 4.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.66 µm / Nominal defocus min: 1.06 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 364869
CTF correctionDetails: Subvloumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 37013
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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