6g5i

From Proteopedia

(Difference between revisions)

Revision as of 06:35, 20 June 2018

Cryo-EM structure of a late human pre-40S ribosomal subunit - State R

Structural highlights

6g5i is a 36 chain structure with sequence from Human and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	PNO1 (HUMAN), NOB1, ART4, NOB1P, PSMD8BP1, MSTP158 (HUMAN), RIOK1 (HUMAN)
Activity:	DNA-(apurinic or apyrimidinic site) lyase, with EC number 4.2.99.18
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[RS19_HUMAN] Blackfan-Diamond disease. Diamond-Blackfan anemia 1 (DBA1) [MIM:105650]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] [REFERENCE:18] [RS24_HUMAN] Blackfan-Diamond disease. Diamond-Blackfan anemia 3 (DBA3) [MIM:610629]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.^[8] [RS14_HUMAN] Myelodysplastic syndrome associated with isolated del(5q) chromosome abnormality. [RS7_HUMAN] Blackfan-Diamond disease. Diamond-Blackfan anemia 8 (DBA8) [MIM:612563]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.^[9] [RS10_HUMAN] Blackfan-Diamond disease. Diamond-Blackfan anemia 9 (DBA9) [MIM:613308]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.^[10] [RS17_HUMAN] Blackfan-Diamond disease. Diamond-Blackfan anemia 4 (DBA4) [MIM:612527]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.^[11] ^[12]

Function

[RACK1_HUMAN] Involved in the recruitment, assembly and/or regulation of a variety of signaling molecules. Interacts with a wide variety of proteins and plays a role in many cellular processes. Component of the 40S ribosomal subunit involved in translational repression. Binds to and stabilizes activated protein kinase C (PKC), increasing PKC-mediated phosphorylation. May recruit activated PKC to the ribosome, leading to phosphorylation of EIF6. Inhibits the activity of SRC kinases including SRC, LCK and YES1. Inhibits cell growth by prolonging the G0/G1 phase of the cell cycle. Enhances phosphorylation of BMAL1 by PRKCA and inhibits transcriptional activity of the BMAL1-CLOCK heterodimer. Facilitates ligand-independent nuclear translocation of AR following PKC activation, represses AR transactivation activity and is required for phosphorylation of AR by SRC. Modulates IGF1R-dependent integrin signaling and promotes cell spreading and contact with the extracellular matrix. Involved in PKC-dependent translocation of ADAM12 to the cell membrane. Promotes the ubiquitination and proteasome-mediated degradation of proteins such as CLEC1B and HIF1A. Required for VANGL2 membrane localization, inhibits Wnt signaling, and regulates cellular polarization and oriented cell division during gastrulation. Required for PTK2/FAK1 phosphorylation and dephosphorylation. Regulates internalization of the muscarinic receptor CHRM2. Promotes apoptosis by increasing oligomerization of BAX and disrupting the interaction of BAX with the anti-apoptotic factor BCL2L. Inhibits TRPM6 channel activity. Regulates cell surface expression of some GPCRs such as TBXA2R. Plays a role in regulation of FLT1-mediated cell migration. Involved in the transport of ABCB4 from the Golgi to the apical bile canalicular membrane (PubMed:19674157). Binds to Y.pseudotuberculosis yopK which leads to inhibition of phagocytosis and survival of bacteria following infection of host cells. Enhances phosphorylation of HIV-1 Nef by PKCs. Promotes migration of breast carcinoma cells by binding to and activating RHOA.^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20] ^[21] ^[22] ^[23] ^[24] ^[25] ^[26] ^[27] ^[28] ^[29] ^[30] ^[31] ^[32] [RS19_HUMAN] Required for pre-rRNA processing and maturation of 40S ribosomal subunits.^[33] [RS24_HUMAN] Required for processing of pre-rRNA and maturation of 40S ribosomal subunits.^[34] [RSSA_HUMAN] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Also functions as a cell surface receptor for laminin. Plays a role in cell adhesion to the basement membrane and in the consequent activation of signaling transduction pathways. May play a role in cell fate determination and tissue morphogenesis. Acts as a PPP1R16B-dependent substrate of PPP1CA. Also acts as a receptor for several other ligands, including the pathogenic prion protein, viruses, and bacteria.^[35] ^[36] ^[37] [RS18_HUMAN] Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity).[HAMAP-Rule:MF_01315] [NOB1_HUMAN] May play a role in mRNA degradation. [RS3A_HUMAN] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122] [RS7_HUMAN] Required for rRNA maturation.^[38] [RS10_HUMAN] Component of the 40S ribosomal subunit. [RS6_HUMAN] May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA. [PNO1_HUMAN] Positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA (PubMed:25851604).^[39]

Publication Abstract from PubMed

The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.

Visualizing late states of human 40S ribosomal subunit maturation.,Ameismeier M, Cheng J, Berninghausen O, Beckmann R Nature. 2018 Jun 6. pii: 10.1038/s41586-018-0193-0. doi:, 10.1038/s41586-018-0193-0. PMID:29875412^[40]

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

References

↑ Angelini M, Cannata S, Mercaldo V, Gibello L, Santoro C, Dianzani I, Loreni F. Missense mutations associated with Diamond-Blackfan anemia affect the assembly of ribosomal protein S19 into the ribosome. Hum Mol Genet. 2007 Jul 15;16(14):1720-7. Epub 2007 May 20. PMID:17517689 doi:ddm120
↑ Da Costa L, Tchernia G, Gascard P, Lo A, Meerpohl J, Niemeyer C, Chasis JA, Fixler J, Mohandas N. Nucleolar localization of RPS19 protein in normal cells and mislocalization due to mutations in the nucleolar localization signals in 2 Diamond-Blackfan anemia patients: potential insights into pathophysiology. Blood. 2003 Jun 15;101(12):5039-45. Epub 2003 Feb 13. PMID:12586610 doi:10.1182/blood-2002-12-3878
↑ Draptchinskaia N, Gustavsson P, Andersson B, Pettersson M, Willig TN, Dianzani I, Ball S, Tchernia G, Klar J, Matsson H, Tentler D, Mohandas N, Carlsson B, Dahl N. The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nat Genet. 1999 Feb;21(2):169-75. PMID:9988267 doi:10.1038/5951
↑ Willig TN, Draptchinskaia N, Dianzani I, Ball S, Niemeyer C, Ramenghi U, Orfali K, Gustavsson P, Garelli E, Brusco A, Tiemann C, Perignon JL, Bouchier C, Cicchiello L, Dahl N, Mohandas N, Tchernia G. Mutations in ribosomal protein S19 gene and diamond blackfan anemia: wide variations in phenotypic expression. Blood. 1999 Dec 15;94(12):4294-306. PMID:10590074
↑ Ramenghi U, Campagnoli MF, Garelli E, Carando A, Brusco A, Bagnara GP, Strippoli P, Izzi GC, Brandalise S, Riccardi R, Dianzani I. Diamond-Blackfan anemia: report of seven further mutations in the RPS19 gene and evidence of mutation heterogeneity in the Italian population. Blood Cells Mol Dis. 2000 Oct;26(5):417-22. PMID:11112378 doi:10.1006/bcmd.2000.0324
↑ Proust A, Da Costa L, Rince P, Landois A, Tamary H, Zaizov R, Tchernia G, Delaunay J. Ten novel Diamond-Blackfan anemia mutations and three polymorphisms within the rps19 gene. Hematol J. 2003;4(2):132-6. PMID:12750732 doi:10.1038/sj.thj.6200230
↑ Gazda HT, Zhong R, Long L, Niewiadomska E, Lipton JM, Ploszynska A, Zaucha JM, Vlachos A, Atsidaftos E, Viskochil DH, Niemeyer CM, Meerpohl JJ, Rokicka-Milewska R, Pospisilova D, Wiktor-Jedrzejczak W, Nathan DG, Beggs AH, Sieff CA. RNA and protein evidence for haplo-insufficiency in Diamond-Blackfan anaemia patients with RPS19 mutations. Br J Haematol. 2004 Oct;127(1):105-13. PMID:15384984 doi:10.1111/j.1365-2141.2004.05152.x
↑ Gazda HT, Grabowska A, Merida-Long LB, Latawiec E, Schneider HE, Lipton JM, Vlachos A, Atsidaftos E, Ball SE, Orfali KA, Niewiadomska E, Da Costa L, Tchernia G, Niemeyer C, Meerpohl JJ, Stahl J, Schratt G, Glader B, Backer K, Wong C, Nathan DG, Beggs AH, Sieff CA. Ribosomal protein S24 gene is mutated in Diamond-Blackfan anemia. Am J Hum Genet. 2006 Dec;79(6):1110-8. Epub 2006 Nov 2. PMID:17186470 doi:10.1086/510020
↑ Gazda HT, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Schneider H, Darras N, Hasman C, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Zaucha JM, Glader B, Niemeyer C, Meerpohl JJ, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH. Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients. Am J Hum Genet. 2008 Dec;83(6):769-80. PMID:19061985 doi:S0002-9297(08)00589-2
↑ Doherty L, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Clinton C, Schneider HE, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Glader B, Arceci RJ, Farrar JE, Atsidaftos E, Lipton JM, Gleizes PE, Gazda HT. Ribosomal protein genes RPS10 and RPS26 are commonly mutated in Diamond-Blackfan anemia. Am J Hum Genet. 2010 Feb 12;86(2):222-8. doi: 10.1016/j.ajhg.2009.12.015. Epub, 2010 Jan 28. PMID:20116044 doi:10.1016/j.ajhg.2009.12.015
↑ Cmejla R, Cmejlova J, Handrkova H, Petrak J, Pospisilova D. Ribosomal protein S17 gene (RPS17) is mutated in Diamond-Blackfan anemia. Hum Mutat. 2007 Dec;28(12):1178-82. PMID:17647292 doi:10.1002/humu.20608
↑ Gazda HT, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Schneider H, Darras N, Hasman C, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Zaucha JM, Glader B, Niemeyer C, Meerpohl JJ, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH. Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients. Am J Hum Genet. 2008 Dec;83(6):769-80. PMID:19061985 doi:S0002-9297(08)00589-2
↑ Gallina A, Rossi F, Milanesi G. Rack1 binds HIV-1 Nef and can act as a Nef-protein kinase C adaptor. Virology. 2001 Apr 25;283(1):7-18. PMID:11312657 doi:10.1006/viro.2001.0855
↑ Hermanto U, Zong CS, Li W, Wang LH. RACK1, an insulin-like growth factor I (IGF-I) receptor-interacting protein, modulates IGF-I-dependent integrin signaling and promotes cell spreading and contact with extracellular matrix. Mol Cell Biol. 2002 Apr;22(7):2345-65. PMID:11884618
↑ Cox EA, Bennin D, Doan AT, O'Toole T, Huttenlocher A. RACK1 regulates integrin-mediated adhesion, protrusion, and chemotactic cell migration via its Src-binding site. Mol Biol Cell. 2003 Feb;14(2):658-69. PMID:12589061 doi:10.1091/mbc.E02-03-0142
↑ Rigas AC, Ozanne DM, Neal DE, Robson CN. The scaffolding protein RACK1 interacts with androgen receptor and promotes cross-talk through a protein kinase C signaling pathway. J Biol Chem. 2003 Nov 14;278(46):46087-93. Epub 2003 Sep 4. PMID:12958311 doi:http://dx.doi.org/10.1074/jbc.M306219200
↑ Kraus S, Gioeli D, Vomastek T, Gordon V, Weber MJ. Receptor for activated C kinase 1 (RACK1) and Src regulate the tyrosine phosphorylation and function of the androgen receptor. Cancer Res. 2006 Nov 15;66(22):11047-54. PMID:17108144 doi:10.1158/0008-5472.CAN-06-0596
↑ Liu YV, Baek JH, Zhang H, Diez R, Cole RN, Semenza GL. RACK1 competes with HSP90 for binding to HIF-1alpha and is required for O(2)-independent and HSP90 inhibitor-induced degradation of HIF-1alpha. Mol Cell. 2007 Jan 26;25(2):207-17. PMID:17244529 doi:10.1016/j.molcel.2007.01.001
↑ Chuang NN, Huang CC. Interaction of integrin beta1 with cytokeratin 1 in neuroblastoma NMB7 cells. Biochem Soc Trans. 2007 Nov;35(Pt 5):1292-4. PMID:17956333 doi:10.1042/BST0351292
↑ Parent A, Laroche G, Hamelin E, Parent JL. RACK1 regulates the cell surface expression of the G protein-coupled receptor for thromboxane A(2). Traffic. 2008 Mar;9(3):394-407. Epub 2007 Dec 14. PMID:18088317 doi:10.1111/j.1600-0854.2007.00692.x
↑ Cao G, Thebault S, van der Wijst J, van der Kemp A, Lasonder E, Bindels RJ, Hoenderop JG. RACK1 inhibits TRPM6 activity via phosphorylation of the fused alpha-kinase domain. Curr Biol. 2008 Feb 12;18(3):168-76. doi: 10.1016/j.cub.2007.12.058. PMID:18258429 doi:10.1016/j.cub.2007.12.058
↑ Bourd-Boittin K, Le Pabic H, Bonnier D, L'Helgoualc'h A, Theret N. RACK1, a new ADAM12 interacting protein. Contribution to liver fibrogenesis. J Biol Chem. 2008 Sep 19;283(38):26000-9. doi: 10.1074/jbc.M709829200. Epub 2008 , Jul 11. PMID:18621736 doi:10.1074/jbc.M709829200
↑ Kiely PA, Baillie GS, Barrett R, Buckley DA, Adams DR, Houslay MD, O'Connor R. Phosphorylation of RACK1 on tyrosine 52 by c-Abl is required for insulin-like growth factor I-mediated regulation of focal adhesion kinase. J Biol Chem. 2009 Jul 24;284(30):20263-74. doi: 10.1074/jbc.M109.017640. Epub, 2009 May 7. PMID:19423701 doi:10.1074/jbc.M109.017640
↑ Ikebuchi Y, Takada T, Ito K, Yoshikado T, Anzai N, Kanai Y, Suzuki H. Receptor for activated C-kinase 1 regulates the cellular localization and function of ABCB4. Hepatol Res. 2009 Nov;39(11):1091-107. doi: 10.1111/j.1872-034X.2009.00544.x., Epub 2009 Aug 6. PMID:19674157 doi:http://dx.doi.org/10.1111/j.1872-034X.2009.00544.x
↑ Ruan Y, Guo L, Qiao Y, Hong Y, Zhou L, Sun L, Wang L, Zhu H, Wang L, Yun X, Xie J, Gu J. RACK1 associates with CLEC-2 and promotes its ubiquitin-proteasome degradation. Biochem Biophys Res Commun. 2009 Dec 11;390(2):217-22. doi:, 10.1016/j.bbrc.2009.09.087. Epub 2009 Sep 26. PMID:19785988 doi:10.1016/j.bbrc.2009.09.087
↑ Cao XX, Xu JD, Xu JW, Liu XL, Cheng YY, Li QQ, Xu ZD, Liu XP. RACK1 promotes breast carcinoma migration/metastasis via activation of the RhoA/Rho kinase pathway. Breast Cancer Res Treat. 2011 Apr;126(3):555-63. doi: 10.1007/s10549-010-0955-3. , Epub 2010 May 25. PMID:20499158 doi:10.1007/s10549-010-0955-3
↑ Wu Y, Wang Y, Sun Y, Zhang L, Wang D, Ren F, Chang D, Chang Z, Jia B. RACK1 promotes Bax oligomerization and dissociates the interaction of Bax and Bcl-XL. Cell Signal. 2010 Oct;22(10):1495-501. doi: 10.1016/j.cellsig.2010.05.018. Epub, 2010 Jun 10. PMID:20541605 doi:10.1016/j.cellsig.2010.05.018
↑ Schaffler K, Schulz K, Hirmer A, Wiesner J, Grimm M, Sickmann A, Fischer U. A stimulatory role for the La-related protein 4B in translation. RNA. 2010 Aug;16(8):1488-99. doi: 10.1261/rna.2146910. Epub 2010 Jun 23. PMID:20573744 doi:10.1261/rna.2146910
↑ Reiner CL, McCullar JS, Kow RL, Le JH, Goodlett DR, Nathanson NM. RACK1 associates with muscarinic receptors and regulates M(2) receptor trafficking. PLoS One. 2010 Oct 20;5(10):e13517. doi: 10.1371/journal.pone.0013517. PMID:20976005 doi:10.1371/journal.pone.0013517
↑ Wang F, Yamauchi M, Muramatsu M, Osawa T, Tsuchida R, Shibuya M. RACK1 regulates VEGF/Flt1-mediated cell migration via activation of a PI3K/Akt pathway. J Biol Chem. 2011 Mar 18;286(11):9097-106. doi: 10.1074/jbc.M110.165605. Epub, 2011 Jan 6. PMID:21212275 doi:10.1074/jbc.M110.165605
↑ Thorslund SE, Edgren T, Pettersson J, Nordfelth R, Sellin ME, Ivanova E, Francis MS, Isaksson EL, Wolf-Watz H, Fallman M. The RACK1 signaling scaffold protein selectively interacts with Yersinia pseudotuberculosis virulence function. PLoS One. 2011 Feb 10;6(2):e16784. doi: 10.1371/journal.pone.0016784. PMID:21347310 doi:10.1371/journal.pone.0016784
↑ Chang BY, Conroy KB, Machleder EM, Cartwright CA. RACK1, a receptor for activated C kinase and a homolog of the beta subunit of G proteins, inhibits activity of src tyrosine kinases and growth of NIH 3T3 cells. Mol Cell Biol. 1998 Jun;18(6):3245-56. PMID:9584165
↑ Flygare J, Aspesi A, Bailey JC, Miyake K, Caffrey JM, Karlsson S, Ellis SR. Human RPS19, the gene mutated in Diamond-Blackfan anemia, encodes a ribosomal protein required for the maturation of 40S ribosomal subunits. Blood. 2007 Feb 1;109(3):980-6. Epub 2006 Sep 21. PMID:16990592 doi:blood-2006-07-038232
↑ Choesmel V, Fribourg S, Aguissa-Toure AH, Pinaud N, Legrand P, Gazda HT, Gleizes PE. Mutation of ribosomal protein RPS24 in Diamond-Blackfan anemia results in a ribosome biogenesis disorder. Hum Mol Genet. 2008 May 1;17(9):1253-63. Epub 2008 Jan 29. PMID:18230666 doi:ddn015
↑ Terranova VP, Rao CN, Kalebic T, Margulies IM, Liotta LA. Laminin receptor on human breast carcinoma cells. Proc Natl Acad Sci U S A. 1983 Jan;80(2):444-8. PMID:6300843
↑ Kim K, Li L, Kozlowski K, Suh HS, Cao W, Ballermann BJ. The protein phosphatase-1 targeting subunit TIMAP regulates LAMR1 phosphorylation. Biochem Biophys Res Commun. 2005 Dec 23;338(3):1327-34. Epub 2005 Oct 25. PMID:16263087 doi:10.1016/j.bbrc.2005.10.089
↑ Kim KJ, Chung JW, Kim KS. 67-kDa laminin receptor promotes internalization of cytotoxic necrotizing factor 1-expressing Escherichia coli K1 into human brain microvascular endothelial cells. J Biol Chem. 2005 Jan 14;280(2):1360-8. Epub 2004 Oct 29. PMID:15516338 doi:M410176200
↑ Gazda HT, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Schneider H, Darras N, Hasman C, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Zaucha JM, Glader B, Niemeyer C, Meerpohl JJ, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH. Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients. Am J Hum Genet. 2008 Dec;83(6):769-80. PMID:19061985 doi:S0002-9297(08)00589-2
↑ Zorbas C, Nicolas E, Wacheul L, Huvelle E, Heurgue-Hamard V, Lafontaine DL. The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis. Mol Biol Cell. 2015 Jun 1;26(11):2080-95. doi: 10.1091/mbc.E15-02-0073. Epub 2015, Apr 7. PMID:25851604 doi:http://dx.doi.org/10.1091/mbc.E15-02-0073
↑ Ameismeier M, Cheng J, Berninghausen O, Beckmann R. Visualizing late states of human 40S ribosomal subunit maturation. Nature. 2018 Jun 6. pii: 10.1038/s41586-018-0193-0. doi:, 10.1038/s41586-018-0193-0. PMID:29875412 doi:http://dx.doi.org/10.1038/s41586-018-0193-0

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6g5i"

@@ Line 3: / Line 3: @@
 <StructureSection load='6g5i' size='340' side='right' caption='[[6g5i]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6g5i]] is a 36 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G5I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6g5i]] is a 36 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G5I FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PNO1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NOB1, ART4, NOB1P, PSMD8BP1, MSTP158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RIOK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></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=6g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g5i OCA], [http://pdbe.org/6g5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g5i RCSB], [http://www.ebi.ac.uk/pdbsum/6g5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g5i ProSAT]</span></td></tr>
@@ Line 12: / Line 13: @@
 == Function ==
 [[http://www.uniprot.org/uniprot/RACK1_HUMAN RACK1_HUMAN]] Involved in the recruitment, assembly and/or regulation of a variety of signaling molecules. Interacts with a wide variety of proteins and plays a role in many cellular processes. Component of the 40S ribosomal subunit involved in translational repression. Binds to and stabilizes activated protein kinase C (PKC), increasing PKC-mediated phosphorylation. May recruit activated PKC to the ribosome, leading to phosphorylation of EIF6. Inhibits the activity of SRC kinases including SRC, LCK and YES1. Inhibits cell growth by prolonging the G0/G1 phase of the cell cycle. Enhances phosphorylation of BMAL1 by PRKCA and inhibits transcriptional activity of the BMAL1-CLOCK heterodimer. Facilitates ligand-independent nuclear translocation of AR following PKC activation, represses AR transactivation activity and is required for phosphorylation of AR by SRC. Modulates IGF1R-dependent integrin signaling and promotes cell spreading and contact with the extracellular matrix. Involved in PKC-dependent translocation of ADAM12 to the cell membrane. Promotes the ubiquitination and proteasome-mediated degradation of proteins such as CLEC1B and HIF1A. Required for VANGL2 membrane localization, inhibits Wnt signaling, and regulates cellular polarization and oriented cell division during gastrulation. Required for PTK2/FAK1 phosphorylation and dephosphorylation. Regulates internalization of the muscarinic receptor CHRM2. Promotes apoptosis by increasing oligomerization of BAX and disrupting the interaction of BAX with the anti-apoptotic factor BCL2L. Inhibits TRPM6 channel activity. Regulates cell surface expression of some GPCRs such as TBXA2R. Plays a role in regulation of FLT1-mediated cell migration. Involved in the transport of ABCB4 from the Golgi to the apical bile canalicular membrane (PubMed:19674157). Binds to Y.pseudotuberculosis yopK which leads to inhibition of phagocytosis and survival of bacteria following infection of host cells. Enhances phosphorylation of HIV-1 Nef by PKCs. Promotes migration of breast carcinoma cells by binding to and activating RHOA.<ref>PMID:11312657</ref> <ref>PMID:11884618</ref> <ref>PMID:12589061</ref> <ref>PMID:12958311</ref> <ref>PMID:17108144</ref> <ref>PMID:17244529</ref> <ref>PMID:17956333</ref> <ref>PMID:18088317</ref> <ref>PMID:18258429</ref> <ref>PMID:18621736</ref> <ref>PMID:19423701</ref> <ref>PMID:19674157</ref> <ref>PMID:19785988</ref> <ref>PMID:20499158</ref> <ref>PMID:20541605</ref> <ref>PMID:20573744</ref> <ref>PMID:20976005</ref> <ref>PMID:21212275</ref> <ref>PMID:21347310</ref> <ref>PMID:9584165</ref>  [[http://www.uniprot.org/uniprot/RS19_HUMAN RS19_HUMAN]] Required for pre-rRNA processing and maturation of 40S ribosomal subunits.<ref>PMID:16990592</ref>  [[http://www.uniprot.org/uniprot/RS24_HUMAN RS24_HUMAN]] Required for processing of pre-rRNA and maturation of 40S ribosomal subunits.<ref>PMID:18230666</ref>  [[http://www.uniprot.org/uniprot/RSSA_HUMAN RSSA_HUMAN]] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Also functions as a cell surface receptor for laminin. Plays a role in cell adhesion to the basement membrane and in the consequent activation of signaling transduction pathways. May play a role in cell fate determination and tissue morphogenesis. Acts as a PPP1R16B-dependent substrate of PPP1CA. Also acts as a receptor for several other ligands, including the pathogenic prion protein, viruses, and bacteria.<ref>PMID:6300843</ref> <ref>PMID:16263087</ref> <ref>PMID:15516338</ref>  [[http://www.uniprot.org/uniprot/RS18_HUMAN RS18_HUMAN]] Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity).[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/NOB1_HUMAN NOB1_HUMAN]] May play a role in mRNA degradation. [[http://www.uniprot.org/uniprot/RS3A_HUMAN RS3A_HUMAN]] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122] [[http://www.uniprot.org/uniprot/RS7_HUMAN RS7_HUMAN]] Required for rRNA maturation.<ref>PMID:19061985</ref>  [[http://www.uniprot.org/uniprot/RS10_HUMAN RS10_HUMAN]] Component of the 40S ribosomal subunit. [[http://www.uniprot.org/uniprot/RS6_HUMAN RS6_HUMAN]] May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA. [[http://www.uniprot.org/uniprot/PNO1_HUMAN PNO1_HUMAN]] Positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA (PubMed:25851604).<ref>PMID:25851604</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.
+Visualizing late states of human 40S ribosomal subunit maturation.,Ameismeier M, Cheng J, Berninghausen O, Beckmann R Nature. 2018 Jun 6. pii: 10.1038/s41586-018-0193-0. doi:, 10.1038/s41586-018-0193-0. PMID:29875412<ref>PMID:29875412</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6g5i" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 17: / Line 27: @@
 </StructureSection>
 [[Category: Homo sapiens]]
+[[Category: Human]]
 [[Category: Ameismeier, M]]
 [[Category: Beckmann, R]]

6g5i

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Revision as of 06:35, 20 June 2018

Cryo-EM structure of a late human pre-40S ribosomal subunit - State R

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