5NWY
2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complex
This is a non-PDB format compatible entry.
Summary for 5NWY
| Entry DOI | 10.2210/pdb5nwy/pdb |
| EMDB information | 3713 |
| Descriptor | VemP nascent chain, 50S ribosomal protein L11, 50S ribosomal protein L13, ... (56 entities in total) |
| Functional Keywords | vemp-src, peptidyltransferase center, ribosomal exit tunnel, helix-loop-helix. ribosome, 70s, ribosome stalling, arrest peptide, ribosome |
| Biological source | Vibrio alginolyticus More |
| Total number of polymer chains | 56 |
| Total formula weight | 2195557.10 |
| Authors | Su, T.,Cheng, J.,Sohmen, D.,Hedman, R.,Berninghausen, O.,von Heijne, G.,Wilson, D.N.,Beckmann, R. (deposition date: 2017-05-08, release date: 2017-07-19, Last modification date: 2024-10-16) |
| Primary citation | Su, T.,Cheng, J.,Sohmen, D.,Hedman, R.,Berninghausen, O.,von Heijne, G.,Wilson, D.N.,Beckmann, R. The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. Elife, 6:-, 2017 Cited by PubMed Abstract: Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome. PubMed: 28556777DOI: 10.7554/eLife.25642 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.9 Å) |
Structure validation
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