6g4w

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

Structural highlights

6g4w is a 31 chain structure with sequence from Homo sapiens. 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

Disease

[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.[1] [2] [BUD23_HUMAN] BUD23 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of BUD23 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease.[3] [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.[4] [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.[5] [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.[6] [7] [8] [9] [10] [11] [12] [REFERENCE:18]

Function

[TSR1_HUMAN] Required during maturation of the 40S ribosomal subunit in the nucleolus. [BUD23_HUMAN] S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N(7) position of a guanine in 18S rRNA (PubMed:25851604). Requires the methyltransferase adapter protein TRM112 for full rRNA methyltransferase activity (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604). Important for biogenesis end export of the 40S ribosomal subunit independent on its methyltransferase activity (PubMed:24086612). Locus-specific steroid receptor coactivator. Potentiates transactivation by glucocorticoid (NR3C1), mineralocorticoid (NR3C2), androgen (AR) and progesterone (PGR) receptors (PubMed:24488492). Required for the maintenance of open chromatin at the TSC22D3/GILZ locus to facilitate NR3C1 loading on the response elements (PubMed:24488492). Required for maintenance of dimethylation on histone H3 'Lys-79' (H3K79me2), although direct histone methyltransferase activity is not observed in vitro (PubMed:24488492).[13] [14] [15] [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).[16] [TR112_HUMAN] Acts as an activator of both rRNA/tRNA and protein methyltransferases (PubMed:25851604). Together with methyltransferase BUD23, methylates the N(7) position of a guanine in 18S rRNA (PubMed:25851604). The heterodimer with HEMK2/N6AMT1 catalyzes N5-methylation of ETF1 on 'Gln-185', using S-adenosyl L-methionine as methyl donor (PubMed:18539146). The heterodimer with ALKBH8 catalyzes the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA species (PubMed:20308323). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production (PubMed:25851604).[17] [18] [19] [RS7_HUMAN] Required for rRNA maturation.[20] [RS24_HUMAN] Required for processing of pre-rRNA and maturation of 40S ribosomal subunits.[21] [BYST_HUMAN] Required for processing of 20S pre-rRNA precursor and biogenesis of 40S ribosomal subunits. May be required for trophinin-dependent regulation of cell adhesion during implantation of human embryos.[22] [23] [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] [RS3A_HUMAN] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122] [RS6_HUMAN] May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA. [RS19_HUMAN] Required for pre-rRNA processing and maturation of 40S ribosomal subunits.[24]

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[25]

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

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See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ Doll A, Grzeschik KH. Characterization of two novel genes, WBSCR20 and WBSCR22, deleted in Williams-Beuren syndrome. Cytogenet Cell Genet. 2001;95(1-2):20-7. doi: 10.1159/000057012. PMID:11978965 doi:http://dx.doi.org/10.1159/000057012
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
  13. ↑ Ounap K, Kasper L, Kurg A, Kurg R. The human WBSCR22 protein is involved in the biogenesis of the 40S ribosomal subunits in mammalian cells. PLoS One. 2013 Sep 23;8(9):e75686. doi: 10.1371/journal.pone.0075686. eCollection, 2013. PMID:24086612 doi:http://dx.doi.org/10.1371/journal.pone.0075686
  14. ↑ Jangani M, Poolman TM, Matthews L, Yang N, Farrow SN, Berry A, Hanley N, Williamson AJ, Whetton AD, Donn R, Ray DW. The methyltransferase WBSCR22/Merm1 enhances glucocorticoid receptor function and is regulated in lung inflammation and cancer. J Biol Chem. 2014 Mar 28;289(13):8931-46. doi: 10.1074/jbc.M113.540906. Epub 2014, Jan 31. PMID:24488492 doi:http://dx.doi.org/10.1074/jbc.M113.540906
  15. ↑ 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
  16. ↑ 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
  17. ↑ Figaro S, Scrima N, Buckingham RH, Heurgue-Hamard V. HemK2 protein, encoded on human chromosome 21, methylates translation termination factor eRF1. FEBS Lett. 2008 Jul 9;582(16):2352-6. doi: 10.1016/j.febslet.2008.05.045. Epub, 2008 Jun 6. PMID:18539146 doi:http://dx.doi.org/10.1016/j.febslet.2008.05.045
  18. ↑ Fu D, Brophy JA, Chan CT, Atmore KA, Begley U, Paules RS, Dedon PC, Begley TJ, Samson LD. Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol Cell Biol. 2010 May;30(10):2449-59. doi: 10.1128/MCB.01604-09. Epub 2010 Mar , 22. PMID:20308323 doi:http://dx.doi.org/10.1128/MCB.01604-09
  19. ↑ 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
  20. ↑ 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
  21. ↑ 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
  22. ↑ Sugihara K, Sugiyama D, Byrne J, Wolf DP, Lowitz KP, Kobayashi Y, Kabir-Salmani M, Nadano D, Aoki D, Nozawa S, Nakayama J, Mustelin T, Ruoslahti E, Yamaguchi N, Fukuda MN. Trophoblast cell activation by trophinin ligation is implicated in human embryo implantation. Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3799-804. Epub 2007 Feb 26. PMID:17360433 doi:http://dx.doi.org/0611516104
  23. ↑ Miyoshi M, Okajima T, Matsuda T, Fukuda MN, Nadano D. Bystin in human cancer cells: intracellular localization and function in ribosome biogenesis. Biochem J. 2007 Jun 15;404(3):373-81. doi: 10.1042/BJ20061597. PMID:17381424 doi:http://dx.doi.org/10.1042/BJ20061597
  24. ↑ 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
  25. ↑ 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

Contents


6g4w, resolution 4.50Å

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