CURI complex / t-UTP complex / UTP-C complex / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / histone-glutamine methyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / box C/D RNA 3'-end processing / Mpp10 complex ...CURI complex / t-UTP complex / UTP-C complex / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / histone-glutamine methyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / regulation of transcription by RNA polymerase I / rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / septum digestion after cytokinesis / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / rDNA heterochromatin / box C/D RNP complex / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / histone glutamine methylation / U4 snRNA binding / U3 snoRNA binding / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / enzyme activator activity / U4/U6 x U5 tri-snRNP complex / maturation of SSU-rRNA / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / proteasome assembly / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic translation / ribosome biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ATPase activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein L1p/L10e family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / Periodic tryptophan protein 2 / P-loop containing nucleoside triphosphate hydrolase ...Ribosomal protein L1p/L10e family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / Periodic tryptophan protein 2 / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / Alpha/beta knot methyltransferases / Ribosomal protein S4/S9 / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal protein S8 superfamily / Nop domain superfamily / Ribosomal protein S15P / Ribosomal protein S8e/ribosomal biogenesis NSA2 / RNA 3'-terminal phosphate cyclase, insert domain superfamily / WD40-repeat-containing domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Small-subunit processome, Utp13 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / RNA 3'-terminal phosphate cyclase type 2 / Ribosomal protein S4, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Fibrillarin, conserved site / HEAT, type 2 / WD40-repeat-containing domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S7p/S5e / Nrap protein domain 6 / EMG1/NEP1 methyltransferase / Krr1 KH1 domain / Ribosomal protein S4/S9 N-terminal domain / S4 domain / Brix domain / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Ribosomal S3Ae family / KOW motif / Ribosomal family S4e / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7e / Nrap protein nucleotidyltransferase domain 4 / Ribosomal protein S8e / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein S15 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S28e / Ribosomal protein S30 / Fcf1 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 3 / Ribosomal protein S7 domain superfamily
Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 21 / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S8-A / 40S ribosomal protein S4-A / 40S ribosomal protein S30-A / 40S ribosomal protein S24-A / 40S ribosomal protein S22-A ...Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 21 / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S8-A / 40S ribosomal protein S4-A / 40S ribosomal protein S30-A / 40S ribosomal protein S24-A / 40S ribosomal protein S22-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / rRNA 2'-O-methyltransferase fibrillarin / Periodic tryptophan protein 2 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 13 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / 40S ribosomal protein S28-A / Pre-rRNA-processing protein PNO1 / gb:1262303: / gb:874346701: / rRNA-processing protein FCF1 / 40S ribosomal protein S5 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 18 / 13 kDa ribonucleoprotein-associated protein / Ribosome biogenesis protein UTP30 / 40S ribosomal protein S27-A / 40S ribosomal protein S1-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S7-A / 40S ribosomal protein S23-A
Biological species
Saccharomyces cerevisiae (baker's yeast)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
Journal: Elife / Year: 2017 Title: Molecular architecture of the 90S small subunit pre-ribosome. Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye / Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#45: Protein
40SribosomalproteinS24-A / Ribosome / RP50
Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#46: Protein
40SribosomalproteinS27-A / Ribosome / RP61 / YS20
Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P35997
#47: Protein
40SribosomalproteinS28-A / Ribosome / S33 / YS27
Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9
#48: Protein
40SribosomalproteinS30-A / Ribosome
Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CX33
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Helical domain ... , 2 types, 2 molecules UAUB
#53: Protein
Helicaldomainprotein
Mass: 137462.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c
#54: Protein
Helicaldomainprotein
Mass: 84015.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c
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Details
Sequence details
(1) For chains AA, AB, AC, AD, AF, AG, E4, S1, U1 and U2, The authors know the sequences, but they ...(1) For chains AA, AB, AC, AD, AF, AG, E4, S1, U1 and U2, The authors know the sequences, but they were unable to assign the sequences to the coordinates. The correct sequences are as follows. chain AA (UNP Q06679 1-776) MSSSLLSVLKEKSRSLKIRNKPVKMTSQERMIVHRCRFVDFTPATITSLAFSHKSNINKLTPSDLRLAIGRSNGNIEIWNPRNNWFQEMVIEGGKDRSIEGLCWSNVNGESLRLFSIGGSTVVTEWDLATGLPLRNYDCNSGVIWSISINDSQDKLSVGCDNGTVVLIDISGGPGVLEHDTILMRQEARVLTLAWKKDDFVIGGCSDGRIRIWSAQKNDENMGRLLHTMKVDKAKKESTLVWSVIYLPRTDQIASGDSTGSIKFWDFQFATLNQSFKAHDADVLCLTTDTDNNYVFSAGVDRKIFQFSQNTNKSQKNNRWVNSSNRLLHGNDIRAICAYQSKGADFLVSGGVEKTLVINSLTSFSNGNYRKMPTVEPYSKNVLVNKEQRLVVSWSESTVKIWTMGTDSSTEQNYKLVCKLTLKDDQNISTCSLSPDGQVLVVGRPSTTKVFHLQPVGNKLKVTKLDNDLLLRTSTKLVKFIDNSKIVICSCEDDVFIVDLESEEDEKPQEVELLEVTSTKSSIKVPYINRINHLEVDQNIAVISRGCGVVDILDLKARISKPLARLNNFITAVHINTSRKSVVVITADNKIYEFNMNLNSEAENEDSESVLTQWSKNNTDNLPKEWKTLKENCVGIFSDIENSSRLWFWGATWISRIDFDVDFPINKRRKQKKRTHEGLTITDESNFMNDEEDDEDDDIDMEISENLNVLLNQGNKIKSTDVQRNEESSGHFFFTDKYKPLLFVDLISSNELAIIERNPLTFHSKQKAFIQPKLVF chain AB (UNP Q04177 1-643) MDSPVLQSAYDPSGQYLCYVTVALDKQRVGVQPTQRATSSGVDTVWNENFLYLEDSKLKVTCLKWVNLASSDTVAIILGMNNGEIWLYSVLANEVTYKFTTGNSYEIKDIDLMGNQLWCIDSSDAFYQFDLLQFKLLQHFRINNCVQLNKLTIVPAGDSVAQLLVASHSISLIDIEEKKVVMTFPGHVSPVSTLQVITNEFFISGAEGDRFLNVYDIHSGMTKCVLVAESDIKELSHSGQADSIAVTTEDGSLEIFVDPLVSSSTKKRGNKSKKSSKKIQIVSKDGRKVPIYNAFINKDLLNVSWLQNATMPYFKNLQWREIPNEYTVEISLNWNNKNKSADRDLHGKDLASATNYVEGNARVTSGDNFKHVDDAIKSWERELTSLEQEQAKPPQANELLTETFGDKLESSTVARISGKKTNLKGSNLKTATTTGTVTVILSQALQSNDHSLLETVLNNRDERVIRDTIFRLKPALAVILLERLAERIARQTHRQGPLNVWVKWCLIIHGGYLVSIPNLMSTLSSLHSTLKRRSDLLPRLLALDARLDCTINKFKTLNYEAGDIHSSEPVVEEDEDDVEYNEELDDAGLIEDGEESYGSEEEEEGDSDNEEEQKHTSSKQDGRLETEQSDGEEEAGYSDVEME chain AC (UNP P53276 1-713) MPSLSQPFRLATLPKIASLSNFSLQADYVQVADGTFNESTNNITLGISGSSISQYIINPTPKLTFDYPIPSTNIITACNAEKGQANIDGNIEASTDDEANNEKTINTQKKRNVEIWAFGLMVNKGNYTLNVITKALEDTTDTSNDHLSESDIDNKAYTGSDEFLSQYKIKAKAKVMSIKIDTKNSLVIAILQNGLIEIFDFKLTLLHSFDISYDNLKYAKWFTENGTEYVFVLCPLQDDKVCYKLLELTDCGSGESSPIKELSSTIIEGFSFENSKLCYQFGKLYKLNQGKIYIYSLPHCQLQQVIEFPMVDKLSPGDDLISFQPVSVNRVLLTVNNVIYLLDLLHCSTLSQRELTHVKTFQLLKSAVINSEKSHNSKTIAIGISTKNGPNPTSSLEIINIDVGTNTLKDSLGKSFQVGNNDSSVILKPLFDDKDINDKRVKCNDVSGDSSVPVLHCNEVIEKLSALQDNDITSFDDIFFKELKIKEEHYTEKDRYISDPGFLNKVLDLIFGKFSGNDYPKTLTFLLTHPLFPLSRTRNLLSLLRDQPRLFKQAIVTCPNLPLNELLEELFSIRNRELLLDISFRILQDFTRDSIKQEMKKLSKLDVQNFIEFITSGGEDSSPECFNPSQSTQLFQLLSLVLDSIGLFSLEGALLENLTLYIDKQVEIAERNTELWNLIDTKGFQHGFASSTFDNGTSQKRALPTYTMEYLDI chain AD (UNP P38882 1-575) MGSSLDLVASFSHDSTRFAFQASVAQKNNVDIYPLNETKDYVVNSSLVSHIDYETNDMKVSDVIFFGWCSDLIDTQSSNIKRKLDEDEGTGESSEQRCENFFVNGFPDGRIVVYSSNGKDIVNIIKNKKEILGADTDESDIWILDSDKVVKKLQYNNSKPLKTFTLVDGKDDEIVHFQILHQNGTLLVCIITKQMVYIVDPSKRRPSTKYSFEISDAVACEFSSDGKYLLIANNEELIAYDLKEDSKLIQSWPVQVKTLKTLDDLIMALTTDGKINNYKIGEADKVCSIVVNEDLEIIDFTPINSKQQVLISWLNVNEPNFESISLKEIETQGYITINKNEKNNADEADQKKLEEKEEEA