6n8l: Difference between revisions

Latest revision as of 15:54, 6 November 2024

Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunitCryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit

6n8l, resolution 3.60Å

Structural highlights

6n8l is a 10 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.6Å
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NMD3_YEAST Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit. Unlikely to play a significant role in nonsense-mediated mRNA decay (NMD).^[1]

Publication Abstract from PubMed

The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome.

Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.,Zhou Y, Musalgaonkar S, Johnson AW, Taylor DW Nat Commun. 2019 Feb 27;10(1):958. doi: 10.1038/s41467-019-08880-0. PMID:30814529^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ho JH, Kallstrom G, Johnson AW. Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit. J Cell Biol. 2000 Nov 27;151(5):1057-66. PMID:11086007
↑ Zhou Y, Musalgaonkar S, Johnson AW, Taylor DW. Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Nat Commun. 2019 Feb 27;10(1):958. doi: 10.1038/s41467-019-08880-0. PMID:30814529 doi:http://dx.doi.org/10.1038/s41467-019-08880-0

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OCA

[1] Ho JH, Kallstrom G, Johnson AW. Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit. J Cell Biol. 2000 Nov 27;151(5):1057-66. PMID:11086007

[2] Zhou Y, Musalgaonkar S, Johnson AW, Taylor DW. Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Nat Commun. 2019 Feb 27;10(1):958. doi: 10.1038/s41467-019-08880-0. PMID:30814529 doi:http://dx.doi.org/10.1038/s41467-019-08880-0

[1]

[2]

@@ Line 3: / Line 3: @@
 <SX load='6n8l' size='340' side='right' viewer='molstar' caption='[[6n8l]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6n8l]] is a 48 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast], [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N8L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6N8L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6n8l]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N8L FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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]] 3.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6n8j|6n8j]], [[6n8k|6n8k]], [[6n8m|6n8m]], [[6n8n|6n8n]], [[6n8o|6n8o]]</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=6n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8l OCA], [https://pdbe.org/6n8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n8l RCSB], [https://www.ebi.ac.uk/pdbsum/6n8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8l ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8l OCA], [http://pdbe.org/6n8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n8l RCSB], [http://www.ebi.ac.uk/pdbsum/6n8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8l ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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/NMD3_YEAST NMD3_YEAST]] Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit. Unlikely to play a significant role in nonsense-mediated mRNA decay (NMD).<ref>PMID:11086007</ref>  [[http://www.uniprot.org/uniprot/BUD20_YEAST BUD20_YEAST]] Involved in positioning the proximal bud pole signal.<ref>PMID:11452010</ref>  [[http://www.uniprot.org/uniprot/RLP24_YEAST RLP24_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles.<ref>PMID:12808088</ref>  [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/NOG1_YEAST NOG1_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit.<ref>PMID:12808088</ref>  [[http://www.uniprot.org/uniprot/IF6_YEAST IF6_YEAST]] Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm. Is also involved in ribosome biogenesis. Associates with pre-60S subunits in the nucleus and is involved in its nuclear export. Cytoplasmic release of TIF6 from 60S subunits and nuclear relocalization is promoted by the GTPase RIA1/EFL1 and by SDO1. Also required for pre-rRNA processing.<ref>PMID:10085284</ref> <ref>PMID:11779510</ref> <ref>PMID:11238882</ref> <ref>PMID:17353896</ref> <ref>PMID:18256024</ref> <ref>PMID:11101899</ref>  [[http://www.uniprot.org/uniprot/MRT4_YEAST MRT4_YEAST]] Involved in mRNA turnover and ribosome assembly. [[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/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA.
+[https://www.uniprot.org/uniprot/NMD3_YEAST NMD3_YEAST] Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit. Unlikely to play a significant role in nonsense-mediated mRNA decay (NMD).<ref>PMID:11086007</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 20: @@
 ==See Also==
+*[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
 *[[Ribosome 3D structures|Ribosome 3D structures]]
+*[[Ribosome biogenesis protein 3D structures|Ribosome biogenesis protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </SX>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Johnson, A W]]
+[[Category: Johnson AW]]
-[[Category: Musalgaonkar, S]]
+[[Category: Musalgaonkar S]]
-[[Category: Taylor, D W]]
+[[Category: Taylor DW]]
-[[Category: Zhou, Y]]
+[[Category: Zhou Y]]
-[[Category: Nmd3]]
-[[Category: Peptidyl transferase center]]
-[[Category: Ribosome]]
-[[Category: Ribosome biogenesis]]

6n8l: Difference between revisions

Latest revision as of 15:54, 6 November 2024

Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunitCryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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6n8l: Difference between revisions

Latest revision as of 15:54, 6 November 2024

Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunitCryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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