+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3452 | |||||||||
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Title | native 40S-ABCE1 complex | |||||||||
Map data | native 40s ABCE1 complex | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
Authors | Heuer A / Beckmann R / Tampe R | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation. Authors: André Heuer / Milan Gerovac / Christian Schmidt / Simon Trowitzsch / Anne Preis / Peter Kötter / Otto Berninghausen / Thomas Becker / Roland Beckmann / Robert Tampé / Abstract: The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the ...The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1. Notably, the movement implies a collision with A-site factors, thus explaining the splitting mechanism. Disruption of key interactions in the post-splitting complex impairs cellular homeostasis. Additionally, the structure of a native post-splitting complex reveals ABCE1 to be part of the 43S initiation complex, suggesting a coordination of termination, recycling, and initiation. | |||||||||
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_3452.map.gz | 195.3 MB | EMDB map data format | |
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Header (meta data) | emd-3452-v30.xml emd-3452.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_3452.png | 47.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3452 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3452 | HTTPS FTP |
-Validation report
Summary document | emd_3452_validation.pdf.gz | 223 KB | Display | EMDB validaton report |
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Full document | emd_3452_full_validation.pdf.gz | 222.1 KB | Display | |
Data in XML | emd_3452_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3452 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3452 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3452.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | native 40s ABCE1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 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 : native 40S-ABCE1 complex
Entire | Name: native 40S-ABCE1 complex |
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Components |
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-Supramolecule #1: native 40S-ABCE1 complex
Supramolecule | Name: native 40S-ABCE1 complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 1.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R3/3 / Material: COPPER/PALLADIUM / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Purified 40S ribosomal subunits were reconstituted with purified, recombinantly expressed ABCE1 |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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