This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6n8k

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit

6n8k, resolution 3.60Å

Structural highlights

6n8k is a 48 chain structure with sequence from Baker's yeast and Saccharomyces cerevisiae (strain atcc 204508 / s288c). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	6n8j, 6n8l, 6n8m, 6n8n, 6n8o
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RL4A_YEAST] Participates in the regulation of the accumulation of its own mRNA.^[1] [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).^[2] [BUD20_YEAST] Involved in positioning the proximal bud pole signal.^[3] [RLP24_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles.^[4] [RL37A_YEAST] Binds to the 23S rRNA (By similarity). [RL5_YEAST] Binds 5S RNA and is required for 60S subunit assembly. [NOG1_YEAST] Involved in the biogenesis of the 60S ribosomal subunit.^[5] [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.^[6] ^[7] ^[8] ^[9] ^[10] ^[11] [MRT4_YEAST] Involved in mRNA turnover and ribosome assembly. [RL25_YEAST] This protein binds to a specific region on the 26S rRNA. [RL11A_YEAST] Binds to 5S ribosomal RNA.

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^[12]

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

References

↑ Presutti C, Ciafre SA, Bozzoni I. The ribosomal protein L2 in S. cerevisiae controls the level of accumulation of its own mRNA. EMBO J. 1991 Aug;10(8):2215-21. PMID:2065661
↑ 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
↑ Ni L, Snyder M. A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell. 2001 Jul;12(7):2147-70. PMID:11452010
↑ Saveanu C, Namane A, Gleizes PE, Lebreton A, Rousselle JC, Noaillac-Depeyre J, Gas N, Jacquier A, Fromont-Racine M. Sequential protein association with nascent 60S ribosomal particles. Mol Cell Biol. 2003 Jul;23(13):4449-60. PMID:12808088
↑ Saveanu C, Namane A, Gleizes PE, Lebreton A, Rousselle JC, Noaillac-Depeyre J, Gas N, Jacquier A, Fromont-Racine M. Sequential protein association with nascent 60S ribosomal particles. Mol Cell Biol. 2003 Jul;23(13):4449-60. PMID:12808088
↑ Sanvito F, Piatti S, Villa A, Bossi M, Lucchini G, Marchisio PC, Biffo S. The beta4 integrin interactor p27(BBP/eIF6) is an essential nuclear matrix protein involved in 60S ribosomal subunit assembly. J Cell Biol. 1999 Mar 8;144(5):823-37. PMID:10085284
↑ Senger B, Lafontaine DL, Graindorge JS, Gadal O, Camasses A, Sanni A, Garnier JM, Breitenbach M, Hurt E, Fasiolo F. The nucle(ol)ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis. Mol Cell. 2001 Dec;8(6):1363-73. PMID:11779510
↑ Basu U, Si K, Warner JR, Maitra U. The Saccharomyces cerevisiae TIF6 gene encoding translation initiation factor 6 is required for 60S ribosomal subunit biogenesis. Mol Cell Biol. 2001 Mar;21(5):1453-62. PMID:11238882 doi:10.1128/MCB.21.5.1453-1462.2001
↑ Menne TF, Goyenechea B, Sanchez-Puig N, Wong CC, Tonkin LM, Ancliff PJ, Brost RL, Costanzo M, Boone C, Warren AJ. The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast. Nat Genet. 2007 Apr;39(4):486-95. Epub 2007 Mar 11. PMID:17353896 doi:ng1994
↑ Ray P, Basu U, Ray A, Majumdar R, Deng H, Maitra U. The Saccharomyces cerevisiae 60 S ribosome biogenesis factor Tif6p is regulated by Hrr25p-mediated phosphorylation. J Biol Chem. 2008 Apr 11;283(15):9681-91. doi: 10.1074/jbc.M710294200. Epub 2008 , Feb 5. PMID:18256024 doi:10.1074/jbc.M710294200
↑ Groft CM, Beckmann R, Sali A, Burley SK. Crystal structures of ribosome anti-association factor IF6. Nat Struct Biol. 2000 Dec;7(12):1156-64. PMID:11101899 doi:10.1038/82017
↑ 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 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6n8k"

@@ Line 1: / Line 1: @@
 ==Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit==
-<StructureSection load='6n8k' size='340' side='right'caption='[[6n8k]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
+<SX load='6n8k' size='340' side='right' viewer='molstar' caption='[[6n8k]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6n8k]] is a 48 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=6N8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N8K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6n8k]] is a 48 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=6N8K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6N8K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6n8j|6n8j]], [[6n8l|6n8l]], [[6n8m|6n8m]], [[6n8n|6n8n]], [[6n8o|6n8o]]</td></tr>
-<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=6n8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8k OCA], [http://pdbe.org/6n8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n8k RCSB], [http://www.ebi.ac.uk/pdbsum/6n8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8k 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=6n8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8k OCA], [http://pdbe.org/6n8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n8k RCSB], [http://www.ebi.ac.uk/pdbsum/6n8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8k ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 26: / Line 26: @@
 <references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: Baker's yeast]]
 [[Category: Large Structures]]

6n8k

From Proteopedia

Current revision

Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox