6n8j

From Proteopedia

(Difference between revisions)

Current revision

Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit

6n8j, resolution 3.50Å

Structural highlights

6n8j is a 49 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:	6n8k, 6n8l, 6n8m, 6n8n, 6n8o
Gene:	RPL5, RPL1, RPL1A, YPL131W, LPI14W (Baker's yeast)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NSA2_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles. Under normal, rapid growth conditions, high levels of NSA2 would allow the progression of pre-60S particles through the ITS2 processing.^[1] ^[2] [RL4A_YEAST] Participates in the regulation of the accumulation of its own mRNA.^[3] [RL11A_YEAST] Binds to 5S ribosomal RNA. [RL5_YEAST] Binds 5S RNA and is required for 60S subunit assembly. [BUD20_YEAST] Involved in positioning the proximal bud pole signal.^[4] [RLP24_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles.^[5] [RL37A_YEAST] Binds to the 23S rRNA (By similarity). [NOG2_YEAST] GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation.^[6] [NOG1_YEAST] Involved in the biogenesis of the 60S ribosomal subunit.^[7] [RL25_YEAST] This protein binds to a specific region on the 26S rRNA. [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.^[8] ^[9] ^[10] ^[11] ^[12] ^[13] [MRT4_YEAST] Involved in mRNA turnover and ribosome assembly.

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^[14]

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

References

↑ Wade CH, Umbarger MA, McAlear MA. The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes. Yeast. 2006 Mar;23(4):293-306. PMID:16544271 doi:http://dx.doi.org/10.1002/yea.1353
↑ Lebreton A, Saveanu C, Decourty L, Jacquier A, Fromont-Racine M. Nsa2 is an unstable, conserved factor required for the maturation of 27 SB pre-rRNAs. J Biol Chem. 2006 Sep 15;281(37):27099-108. Epub 2006 Jul 21. PMID:16861225 doi:http://dx.doi.org/M602199200
↑ 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
↑ 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, Bienvenu D, Namane A, Gleizes PE, Gas N, Jacquier A, Fromont-Racine M. Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps. EMBO J. 2001 Nov 15;20(22):6475-84. PMID:11707418 doi:http://dx.doi.org/10.1093/emboj/20.22.6475
↑ 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/6n8j"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6n8j is ON HOLD
+==Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit==
+<SX load='6n8j' size='340' side='right' viewer='molstar' caption='[[6n8j]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6n8j]] is a 49 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=6N8J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6N8J FirstGlance]. <br>
+</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">[[6n8k|6n8k]], [[6n8l|6n8l]], [[6n8m|6n8m]], [[6n8n|6n8n]], [[6n8o|6n8o]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPL5, RPL1, RPL1A, YPL131W, LPI14W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6n8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8j OCA], [http://pdbe.org/6n8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n8j RCSB], [http://www.ebi.ac.uk/pdbsum/6n8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/NSA2_YEAST NSA2_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles. Under normal, rapid growth conditions, high levels of NSA2 would allow the progression of pre-60S particles through the ITS2 processing.<ref>PMID:16544271</ref> <ref>PMID:16861225</ref>  [[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/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[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/NOG2_YEAST NOG2_YEAST]] GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation.<ref>PMID:11707418</ref>  [[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/RL25_YEAST RL25_YEAST]] This protein binds to a specific region on the 26S rRNA. [[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.
+<div style="background-color:#fffaf0;">
+== 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.
-Authors:
+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<ref>PMID:30814529</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6n8j" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+== References ==
+<references/>
+__TOC__
+</SX>
+[[Category: Baker's yeast]]
+[[Category: Large Structures]]
+[[Category: Johnson, A W]]
+[[Category: Musalgaonkar, S]]
+[[Category: Taylor, D W]]
+[[Category: Zhou, Y]]
+[[Category: Nmd3]]
+[[Category: Peptidyl transferase center]]
+[[Category: Ribosome]]
+[[Category: Ribosome biogenesis]]

6n8j

From Proteopedia

Current revision

Cryo-EM structure of late nuclear (LN) 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