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.

5h4p

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 20:10, 10 April 2020

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1

5h4p, resolution 3.07Å

Structural highlights

5h4p is a 44 chain structure with sequence from Saccharomyces cerevisiae and Saccharomyces cerevisiae (strain atcc 204508 / s288c). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RL5_YEAST] Binds 5S RNA and is required for 60S subunit assembly. [REH1_YEAST] Pre-60S-associated cytoplasmic factor involved in the cytoplasmic maturation of the 60S subunit. May act redundantly with REI1 to directly promote a stabilizing structural rearrangement in cytoplasmic 60S subunit maturation independent on the REI1-specific ARX1 recycling.^[1] [RL25_YEAST] This protein binds to a specific region on the 26S rRNA. [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] [RL4A_YEAST] Participates in the regulation of the accumulation of its own mRNA.^[3] [RL11A_YEAST] Binds to 5S ribosomal RNA. [RL37A_YEAST] Binds to the 23S rRNA (By similarity). [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.^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. Here we used cryo-electron microscopy (cryo-EM) to characterize Saccharomyces cerevisiae pre-60S particles purified with epitope-tagged Nmd3. Our structural analysis indicates that these particles belong to a specific late stage of cytoplasmic pre-60S maturation in which ribosomal proteins uL16, uL10, uL11, eL40 and eL41 are deficient, but ribosome assembly factors Nmd3, Lsg1, Tif6 and Reh1 are present. Nmd3 and Lsg1 are located near the peptidyl-transferase center (PTC). In particular, Nmd3 recognizes the PTC in its near-mature conformation. In contrast, Reh1 is anchored to the exit of the polypeptide tunnel, with its C terminus inserted into the tunnel. These findings pinpoint a structural checkpoint role for Nmd3 in PTC assembly, and provide information about functional and mechanistic roles of these assembly factors in the maturation of the 60S ribosomal subunit.

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1.,Ma C, Wu S, Li N, Chen Y, Yan K, Li Z, Zheng L, Lei J, Woolford JL Jr, Gao N Nat Struct Mol Biol. 2017 Mar;24(3):214-220. doi: 10.1038/nsmb.3364. Epub 2017, Jan 23. PMID:28112732^[10]

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

References

↑ Parnell KM, Bass BL. Functional redundancy of yeast proteins Reh1 and Rei1 in cytoplasmic 60S subunit maturation. Mol Cell Biol. 2009 Jul;29(14):4014-23. Epub 2009 May 11. PMID:19433447 doi:http://dx.doi.org/MCB.01582-08
↑ 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
↑ 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
↑ 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
↑ Ma C, Wu S, Li N, Chen Y, Yan K, Li Z, Zheng L, Lei J, Woolford JL Jr, Gao N. Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1. Nat Struct Mol Biol. 2017 Mar;24(3):214-220. doi: 10.1038/nsmb.3364. Epub 2017, Jan 23. PMID:28112732 doi:http://dx.doi.org/10.1038/nsmb.3364

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5h4p"

Categories: Large Structures | Saccharomyces cerevisiae | Chen, Y | Gao, N | Lei, J | Li, N | Li, Z | Ma, C | Woolford, J L | Wu, S | Yan, K | Zheng, L | Assembly | Lsg1 | Nmd3 | Pre-60 | Ribosome

@@ Line 3: / Line 3: @@
 <SX load='5h4p' size='340' side='right' viewer='molstar' caption='[[5h4p]], [[Resolution|resolution]] 3.07&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5h4p]] is a 44 chain structure with sequence from [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=5H4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H4P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5h4p]] is a 44 chain structure with sequence from [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=5H4P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H4P FirstGlance]. <br>
-</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=5h4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h4p OCA], [http://pdbe.org/5h4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h4p RCSB], [http://www.ebi.ac.uk/pdbsum/5h4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h4p ProSAT]</span></td></tr>
+</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=5h4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h4p OCA], [http://pdbe.org/5h4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h4p RCSB], [http://www.ebi.ac.uk/pdbsum/5h4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h4p ProSAT]</span></td></tr>
 </table>
 == Function ==

5h4p

From Proteopedia

Revision as of 20:10, 10 April 2020

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox