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TitleCryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 17, Page 8909-8924, Year 2023
Publish dateSep 22, 2023
AuthorsYing-Hui Wang / Hong Dai / Ling Zhang / Yun Wu / Jingfen Wang / Chen Wang / Cai-Huang Xu / Hai Hou / Bing Yang / Yongqun Zhu / Xing Zhang / Jie Zhou /
PubMed AbstractArchaeal 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 ...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.
External linksNucleic Acids Res / PubMed:37604686 / PubMed Central
MethodsEM (single particle)
Resolution3.93 - 4.8 Å
Structure data

34864

8hkz

EMDB-34864, PDB-8hkz:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.78 Å

34866

8hl1

EMDB-34866, PDB-8hl1:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 3.93 Å

34867

8hl2

EMDB-34867, PDB-8hl2:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.1 Å

34868

8hl3

EMDB-34868, PDB-8hl3:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.8 Å

Chemicals

ChemComp-UNK:
UNKNOWN

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

Source
  • sulfolobus acidocaldarius dsm 639 (acidophilic)
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome / Sulfolobus acidocaldarius ribosome small subunit

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