8HKU

Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome

This is a non-PDB format compatible entry.

Summary for 8HKU

• Entry DOI: 10.2210/pdb8hku/pdb
• EMDB information: 34860
• Descriptor: 23s rRNA (2996-MER), 50S ribosomal protein L10e, 50S ribosomal protein L13, ... (40 entities in total)
• Functional Keywords: sulfolobus acidocaldarius ribosome small subunit, ribosome
• Biological source: Sulfolobus acidocaldarius DSM 639; More
• Total number of polymer chains: 42
• Total formula weight: 1591265.68

Authors

Wang, Y.H.,Zhou, J. (deposition date: 2022-11-28, release date: 2023-08-16, Last modification date: 2024-11-06)

Primary citation

Wang, Y.H.,Dai, H.,Zhang, L.,Wu, Y.,Wang, J.,Wang, C.,Xu, C.H.,Hou, H.,Yang, B.,Zhu, Y.,Zhang, X.,Zhou, J.
Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Nucleic Acids Res., 51:8909-8924, 2023

PubMed Abstract: Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.

PubMed: 37604686
DOI: 10.1093/nar/gkad661

Experimental method

ELECTRON MICROSCOPY (2.72 Å)