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Structural highlights
5jcs is a 48 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Gene: | RPL2A, RPL5B, YFR031C-A, YFR031BC (Baker's yeast), RPL34A, YER056C-A, YER056BC (Baker's yeast), RPL7A, RPL6A, RPL8A, YL8A, YGL076C (Baker's yeast), RPL35A, SOS1, YDL191W, D1249 (Baker's yeast), RPL8A, MAK7, RPL4A, YHL033C (Baker's yeast), RPL36A, RPL39A, YMR194W, YM9646.06 (Baker's yeast), RPL9A, RPL8A, RPL9, YGL147C (Baker's yeast), RPL37A, RPL35A, YLR185W, L9470.6 (Baker's yeast), RPL1A, SSM1, SSM1A, YPL220W (Baker's yeast), RPL38, YLR325C, L8543.2 (Baker's yeast), RPL11A, RP39A, RPL16A, YPR102C, P8283.14 (Baker's yeast), RPL30, RPL32, YGL030W (Baker's yeast), RPL39, RPL46, SPB2, YJL189W, J0360 (Baker's yeast), RPL12A, RPL15B, YEL054C (Baker's yeast), TIF6, CDC95, YPR016C, LPZ15C (Baker's yeast), RPL13A, YDL082W (Baker's yeast), MRT4, YKL009W, YKL160 (Baker's yeast), RPL14A, YKL006W, YKL153 (Baker's yeast), NOG1, YPL093W, LPG15W (Baker's yeast), RPL15A, RPL10A, RPL13A, YL10A, YLR029C (Baker's yeast), RPL43A, YPR043W, YP9499.02 (Baker's yeast), RPL16A, RPL13, RPL21A, YIL133C (Baker's yeast), RPL3, MAK8, TCM1, YOR063W, YOR29-14 (Baker's yeast), RSA4, YCR072C, YCR72C (Baker's yeast), RPL17A, RPL17, RPL20A, YKL180W (Baker's yeast), SDA1, YGR245C (Baker's yeast), RPL18A, RP28A, YOL120C (Baker's yeast), MDN1, REA1, YLR106C, L2901, L8004.13 (Baker's yeast), RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC (Baker's yeast), RLP24, YLR009W (Baker's yeast), RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C (Baker's yeast), ARX1, YDR101C, YD8557.10c (Baker's yeast), RPL21A, URP1, YBR191W, YBR1401 (Baker's yeast), RPL31A, RPL34, RPL34A, YDL075W, D2478 (Baker's yeast), RPL22A, YLR061W, L2168 (Baker's yeast), RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713 (Baker's yeast), RPL25, YOL127W (Baker's yeast), RPL26A, RPL26, RPL33A, YLR344W, L8300.4 (Baker's yeast), RPL27A, RPL27, YHR010W (Baker's yeast), RPL28, CYH2, YGL103W (Baker's yeast), RPL4A, RPL2, RPL2A, YBR031W, YBR0315 (Baker's yeast), RPL32, YBL092W, YBL0838 (Baker's yeast), RPL5, RPL1, RPL1A, YPL131W, LPI14W (Baker's yeast), RPL33A, RPL37A, YPL143W, LPI4W, P2625 (Baker's yeast), RPL6A, RPL17A, YL16A, YML073C (Baker's yeast) |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[SDA1_YEAST] Required for 60S pre-ribosomal subunits export to the cytoplasm. May also be required for 60S ribosomal subunit maturation and accumulation. Involved in G1 events and passage through start, and possibly actin cytoskeleton organization.[1] [2] [3] [4] [5] [RL12A_YEAST] This protein binds directly to 26S ribosomal RNA.[HAMAP-Rule:MF_00736] [RL5_YEAST] Binds 5S RNA and is required for 60S subunit assembly. [NOG1_YEAST] Involved in the biogenesis of the 60S ribosomal subunit.[6] [NLE1_YEAST] Involved in processing and efficient intra-nuclear transport or pre-60S ribosomal subunits. Forms a complex with REA1 which is essential for ATP-dependent dissociation of a group of nonribosomal factors from the pre-60S particle.[7] [8] [9] [RL37A_YEAST] Binds to the 23S rRNA (By similarity). [MRT4_YEAST] Involved in mRNA turnover and ribosome assembly. [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.[10] [11] [12] [13] [14] [15] [RLP24_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles.[16] [ARX1_YEAST] Probable metalloprotease involved in proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. Accompanies the pre-60S particles to the cytoplasm.[17] [18] [MDN1_YEAST] Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits. Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre-60S particles from the nucleolus and then driving late pre-60S particles from the nucleus. Mediates ATP-dependent remodeling of the pre-ribosome just prior to export to allow maturation of 60S subunits into export-competent particles. Removes the ribosome biogenesis factor RSA4 from pre-60S ribosomal subunits in the nucleoplasm to drive nuclear export of the subunit. Involved in 3' processing of the 5.8S rRNA.[19] [20] [21] [22] [RL25_YEAST] This protein binds to a specific region on the 26S rRNA. [RL11A_YEAST] Binds to 5S ribosomal RNA. [RL4A_YEAST] Participates in the regulation of the accumulation of its own mRNA.[23]
Publication Abstract from PubMed
Ribosome synthesis is catalyzed by approximately 200 assembly factors, which facilitate efficient production of mature ribosomes. Here, we determined the cryo-EM structure of a Saccharomyces cerevisiae nucleoplasmic pre-60S particle containing the dynein-related 550-kDa Rea1 AAA(+) ATPase and the Rix1 subcomplex. This particle differs from its preceding state, the early Arx1 particle, by two massive structural rearrangements: an approximately 180 degrees rotation of the 5S ribonucleoprotein complex and the central protuberance (CP) rRNA helices, and the removal of the 'foot' structure from the 3' end of the 5.8S rRNA. Progression from the Arx1 to the Rix1 particle was blocked by mutational perturbation of the Rix1-Rea1 interaction but not by a dominant-lethal Rea1 AAA(+) ATPase-ring mutant. After remodeling, the Rix1 subcomplex and Rea1 become suitably positioned to sense correct structural maturation of the CP, which allows unidirectional progression toward mature ribosomes.
Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.,Barrio-Garcia C, Thoms M, Flemming D, Kater L, Berninghausen O, Bassler J, Beckmann R, Hurt E Nat Struct Mol Biol. 2016 Jan;23(1):37-44. doi: 10.1038/nsmb.3132. Epub 2015 Nov , 30. PMID:26619264[24]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Buscemi G, Saracino F, Masnada D, Carbone ML. The Saccharomyces cerevisiae SDA1 gene is required for actin cytoskeleton organization and cell cycle progression. J Cell Sci. 2000 Apr;113 ( Pt 7):1199-211. PMID:10704371
- ↑ Zimmerman ZA, Kellogg DR. The Sda1 protein is required for passage through start. Mol Biol Cell. 2001 Jan;12(1):201-19. PMID:11160833
- ↑ Nissan TA, Bassler J, Petfalski E, Tollervey D, Hurt E. 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm. EMBO J. 2002 Oct 15;21(20):5539-47. PMID:12374754
- ↑ Saracino F, Bassler J, Muzzini D, Hurt E, Agostoni Carbone ML. The yeast kinase Swe1 is required for proper entry into cell cycle after arrest due to ribosome biogenesis and protein synthesis defects. Cell Cycle. 2004 May;3(5):648-54. Epub 2004 May 15. PMID:15107621
- ↑ Dez C, Houseley J, Tollervey D. Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J. 2006 Apr 5;25(7):1534-46. Epub 2006 Mar 16. PMID:16541108 doi:https://dx.doi.org/10.1038/sj.emboj.7601035
- ↑ 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
- ↑ de la Cruz J, Sanz-Martinez E, Remacha M. The essential WD-repeat protein Rsa4p is required for rRNA processing and intra-nuclear transport of 60S ribosomal subunits. Nucleic Acids Res. 2005 Oct 12;33(18):5728-39. Print 2005. PMID:16221974 doi:https://dx.doi.org/10.1093/nar/gki887
- ↑ Ulbrich C, Diepholz M, Bassler J, Kressler D, Pertschy B, Galani K, Bottcher B, Hurt E. Mechanochemical removal of ribosome biogenesis factors from nascent 60S ribosomal subunits. Cell. 2009 Sep 4;138(5):911-22. PMID:19737519 doi:https://dx.doi.org/S0092-8674(09)00792-2
- ↑ Bassler J, Kallas M, Pertschy B, Ulbrich C, Thoms M, Hurt E. The AAA-ATPase Rea1 drives removal of biogenesis factors during multiple stages of 60S ribosome assembly. Mol Cell. 2010 Jun 11;38(5):712-21. doi: 10.1016/j.molcel.2010.05.024. PMID:20542003 doi:https://dx.doi.org/10.1016/j.molcel.2010.05.024
- ↑ 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
- ↑ 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
- ↑ Nissan TA, Bassler J, Petfalski E, Tollervey D, Hurt E. 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm. EMBO J. 2002 Oct 15;21(20):5539-47. PMID:12374754
- ↑ Hung NJ, Johnson AW. Nuclear recycling of the pre-60S ribosomal subunit-associated factor Arx1 depends on Rei1 in Saccharomyces cerevisiae. Mol Cell Biol. 2006 May;26(10):3718-27. PMID:16648468 doi:https://dx.doi.org/26/10/3718
- ↑ Nissan TA, Galani K, Maco B, Tollervey D, Aebi U, Hurt E. A pre-ribosome with a tadpole-like structure functions in ATP-dependent maturation of 60S subunits. Mol Cell. 2004 Jul 23;15(2):295-301. PMID:15260980 doi:https://dx.doi.org/10.1016/j.molcel.2004.06.033
- ↑ Galani K, Nissan TA, Petfalski E, Tollervey D, Hurt E. Rea1, a dynein-related nuclear AAA-ATPase, is involved in late rRNA processing and nuclear export of 60 S subunits. J Biol Chem. 2004 Dec 31;279(53):55411-8. Epub 2004 Nov 3. PMID:15528184 doi:https://dx.doi.org/10.1074/jbc.M406876200
- ↑ Ulbrich C, Diepholz M, Bassler J, Kressler D, Pertschy B, Galani K, Bottcher B, Hurt E. Mechanochemical removal of ribosome biogenesis factors from nascent 60S ribosomal subunits. Cell. 2009 Sep 4;138(5):911-22. PMID:19737519 doi:https://dx.doi.org/S0092-8674(09)00792-2
- ↑ Bassler J, Kallas M, Pertschy B, Ulbrich C, Thoms M, Hurt E. The AAA-ATPase Rea1 drives removal of biogenesis factors during multiple stages of 60S ribosome assembly. Mol Cell. 2010 Jun 11;38(5):712-21. doi: 10.1016/j.molcel.2010.05.024. PMID:20542003 doi:https://dx.doi.org/10.1016/j.molcel.2010.05.024
- ↑ 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
- ↑ Barrio-Garcia C, Thoms M, Flemming D, Kater L, Berninghausen O, Bassler J, Beckmann R, Hurt E. Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling. Nat Struct Mol Biol. 2016 Jan;23(1):37-44. doi: 10.1038/nsmb.3132. Epub 2015 Nov , 30. PMID:26619264 doi:https://dx.doi.org/10.1038/nsmb.3132
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