4v4b

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==Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.==
==Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.==
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<StructureSection load='4v4b' size='340' side='right'caption='[[4v4b]], [[Resolution|resolution]] 11.70&Aring;' scene=''>
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<SX load='4v4b' size='340' side='right' viewer='molstar' caption='[[4v4b]], [[Resolution|resolution]] 11.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4v4b]] is a 47 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1s1h 1s1h] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1s1i 1s1i]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V4B FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4v4b]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1s1h 1s1h] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1s1i 1s1i]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V4B FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k5x|1k5x]], [[1k5y|1k5y]], [[1mms|1mms]], [[1mzp|1mzp]], [[1ffk|1ffk]], [[1fjf|1fjf]], [[1fka|1fka]], [[1gix|1gix]], [[1giy|1giy]], [[1nou|1nou]]</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 11.7&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4v4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4b OCA], [http://pdbe.org/4v4b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v4b RCSB], [http://www.ebi.ac.uk/pdbsum/4v4b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4b ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4v4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4b OCA], [https://pdbe.org/4v4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v4b RCSB], [https://www.ebi.ac.uk/pdbsum/4v4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RL4A_YEAST RL4A_YEAST]] Participates in the regulation of the accumulation of its own mRNA.<ref>PMID:2065661</ref> [[http://www.uniprot.org/uniprot/RS15_YEAST RS15_YEAST]] Involved in the nuclear export of the small ribosomal subunit. Has a role in the late stage of the assembly of pre-40S particles within the nucleus and controls their export to the cytoplasm.<ref>PMID:15167894</ref> [[http://www.uniprot.org/uniprot/RS9B_YEAST RS9B_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RL4B_YEAST RL4B_YEAST]] Participates in the regulation of the accumulation of its own mRNA. [[http://www.uniprot.org/uniprot/RS2_YEAST RS2_YEAST]] Important in the assembly and function of the 40S ribosomal subunit. Mutations in this protein affects the control of translational fidelity. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RL25_YEAST RL25_YEAST]] This protein binds to a specific region on the 26S rRNA. [[http://www.uniprot.org/uniprot/RSSA1_YEAST RSSA1_YEAST]] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits.<ref>PMID:9973221</ref> <ref>PMID:14627813</ref> [[http://www.uniprot.org/uniprot/RS19A_YEAST RS19A_YEAST]] Required for proper maturation of the small (40S) ribosomal subunit. Binds to 40s pre-ribosomal particles, probably required after association of NOC4 but before association of ENP1, TSR1 and RIO2 with 20/21S pre-rRNA.<ref>PMID:16159874</ref> <ref>PMID:17726054</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref>
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[https://www.uniprot.org/uniprot/EF2_YEAST EF2_YEAST]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.
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Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.,Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jorgensen R, Andersen GR, Beckmann R, Penczek PA, Ballesta JP, Frank J EMBO J. 2004 Mar 10;23(5):1008-19. Epub 2004 Feb 19. PMID:14976550<ref>PMID:14976550</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4v4b" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Ribosomal protein S22|Ribosomal protein S22]]
*[[Ribosomal protein S22|Ribosomal protein S22]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
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</StructureSection>
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</SX>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Andersen, G R]]
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[[Category: Andersen GR]]
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[[Category: Ballesta, J P.G]]
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[[Category: Ballesta JPG]]
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[[Category: Beckmann, R]]
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[[Category: Beckmann R]]
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[[Category: Frank, J]]
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[[Category: Frank J]]
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[[Category: Gomez-Lorenzo, M G]]
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[[Category: Gomez-Lorenzo MG]]
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[[Category: Grassucci, R A]]
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[[Category: Grassucci RA]]
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[[Category: Jorgensen, R]]
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[[Category: Jorgensen R]]
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[[Category: Penczek, P A]]
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[[Category: Penczek PA]]
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[[Category: Spahn, C M]]
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[[Category: Spahn CM]]
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[[Category: 40s ribosomal subunit]]
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[[Category: 80s ribosome]]
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[[Category: Cryo-em]]
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[[Category: Eef2]]
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[[Category: Ribosome]]
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[[Category: Sordarin]]
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[[Category: Trna translocation]]
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Current revision

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.

4v4b, resolution 11.70Å

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