8BTD

Giardia Ribosome in PRE-T Hybrid State (D1)

This is a non-PDB format compatible entry.

Summary for 8BTD

• Entry DOI: 10.2210/pdb8btd/pdb
• EMDB information: 16228
• Descriptor: Ribosomal protein L2, Ribosomal protein L6, Ribosomal protein L10, ... (78 entities in total)
• Functional Keywords: ribosome, translation, giardia, eukaryote, eukaryotic, macromolecule, trna
• Biological source: Giardia lamblia ATCC 50803; More
• Total number of polymer chains: 78
• Total formula weight: 2759171.52

Authors

Majumdar, S.,Emmerich, A.G.,Sanyal, S. (deposition date: 2022-11-28, release date: 2023-03-22, Last modification date: 2024-10-23)

Primary citation

Majumdar, S.,Emmerich, A.,Krakovka, S.,Mandava, C.S.,Svard, S.G.,Sanyal, S.
Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
Nucleic Acids Res., 51:3436-3451, 2023

PubMed Abstract: Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.

PubMed: 36912103
DOI: 10.1093/nar/gkad176

Experimental method

ELECTRON MICROSCOPY (4.9 Å)