+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0203 | |||||||||
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Title | Cryo-EM structure of a RNaseI treated 80S ribosome | |||||||||
Map data | RNaseI treated uL4-RNCs. | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Knorr AG / Berninghausen O / Becker T / Beckmann R | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Authors: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann / Abstract: The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. ...The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation. | |||||||||
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_0203.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-0203-v30.xml emd-0203.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_0203.png | 180.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0203 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0203 | 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_0203.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNaseI treated uL4-RNCs. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.252 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 : RNaseI treated uL4-RNCs
Entire | Name: RNaseI treated uL4-RNCs |
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Components |
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-Supramolecule #1: RNaseI treated uL4-RNCs
Supramolecule | Name: RNaseI treated uL4-RNCs / type: complex / ID: 1 / Parent: 0 Details: Amongst others, features like expansion segment are missing. |
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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
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0beta) / Number images used: 5909 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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