+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4096 | |||||||||
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Title | Cryo-EM structure of the Yvh1 pre-60S particle | |||||||||
Map data | Yvh1 pre-60S particle | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
Authors | Sarkar A / Pech M / Thoms M / Beckmann R / Hurt E | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4096.map.gz | 264.2 MB | EMDB map data format | |
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Header (meta data) | emd-4096-v30.xml emd-4096.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_4096.png | 54 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4096 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4096 | HTTPS FTP |
-Validation report
Summary document | emd_4096_validation.pdf.gz | 292.7 KB | Display | EMDB validaton report |
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Full document | emd_4096_full_validation.pdf.gz | 291.9 KB | Display | |
Data in XML | emd_4096_validation.xml.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4096 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4096 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4096.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yvh1 pre-60S particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.062 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yvh1 pre-60S particle
Entire | Name: Yvh1 pre-60S particle |
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Components |
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-Supramolecule #1: Yvh1 pre-60S particle
Supramolecule | Name: Yvh1 pre-60S particle / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Details: Method Blot for 3 seconds before plunging. | ||||||||||||
Details | The freshly prepared pre-60S sample was applied to 2 nm pre-coated Quantifoil holey carbon supparted grids an vitrified |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3226 / Average electron dose: 4.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.66 µm / Nominal defocus min: 1.06 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |