8hl3: Difference between revisions
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<table><tr><td colspan='2'>[[8hl3]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius_DSM_639 Sulfolobus acidocaldarius DSM 639]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8HL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8HL3 FirstGlance]. <br> | <table><tr><td colspan='2'>[[8hl3]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius_DSM_639 Sulfolobus acidocaldarius DSM 639]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8HL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8HL3 FirstGlance]. <br> | ||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.8Å</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.8Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8hl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8hl3 OCA], [https://pdbe.org/8hl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8hl3 RCSB], [https://www.ebi.ac.uk/pdbsum/8hl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8hl3 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8hl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8hl3 OCA], [https://pdbe.org/8hl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8hl3 RCSB], [https://www.ebi.ac.uk/pdbsum/8hl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8hl3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/EF2_SULAC EF2_SULAC] Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome (By similarity). | [https://www.uniprot.org/uniprot/EF2_SULAC EF2_SULAC] Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome (By similarity). | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 A 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 degrees 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. | |||
Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.,Wang YH, Dai H, Zhang L, Wu Y, Wang J, Wang C, Xu CH, Hou H, Yang B, Zhu Y, Zhang X, Zhou J Nucleic Acids Res. 2023 Sep 22;51(17):8909-8924. doi: 10.1093/nar/gkad661. PMID:37604686<ref>PMID:37604686</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 8hl3" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Ribosome 3D structures|Ribosome 3D structures]] | *[[Ribosome 3D structures|Ribosome 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Latest revision as of 09:33, 5 February 2025
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota RibosomeCryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Structural highlights
FunctionEF2_SULAC Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome (By similarity). Publication Abstract from PubMedArchaeal 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 A 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 degrees 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. Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.,Wang YH, Dai H, Zhang L, Wu Y, Wang J, Wang C, Xu CH, Hou H, Yang B, Zhu Y, Zhang X, Zhou J Nucleic Acids Res. 2023 Sep 22;51(17):8909-8924. doi: 10.1093/nar/gkad661. PMID:37604686[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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