- EMDB-11519: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G -
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基本情報
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データベース: EMDB / ID: EMD-11519
タイトル
Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
マップデータ
試料
複合体: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
RNA: x 1種
タンパク質・ペプチド: x 36種
リガンド: x 3種
機能・相同性
機能・相同性情報
methyltransferase complex / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・物質の膜輸送を触媒する / positive regulation of rRNA processing / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair ...methyltransferase complex / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・物質の膜輸送を触媒する / positive regulation of rRNA processing / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / ion channel inhibitor activity / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / monocyte chemotaxis / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / T cell proliferation involved in immune response / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Protein methylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation regulator activity / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of cell cycle / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / stress granule assembly / Mitotic Prometaphase / cytosolic ribosome / laminin binding / EML4 and NUDC in mitotic spindle formation / 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) / rough endoplasmic reticulum 類似検索 - 分子機能
Probable RNA-binding protein EIF1AD / Serine/threonine-protein kinase Rio1 / : / Putative WW-binding domain and destruction box / Putative WW-binding domain and destruction box / Nin one binding (NOB1) Zn-ribbon-like / Ribonuclease Nob1, eukaryote / NOB1 zinc finger-like superfamily / Nin one binding (NOB1) Zn-ribbon like / Ribonuclease, PIN domain ...Probable RNA-binding protein EIF1AD / Serine/threonine-protein kinase Rio1 / : / Putative WW-binding domain and destruction box / Putative WW-binding domain and destruction box / Nin one binding (NOB1) Zn-ribbon-like / Ribonuclease Nob1, eukaryote / NOB1 zinc finger-like superfamily / Nin one binding (NOB1) Zn-ribbon like / Ribonuclease, PIN domain / RNA-binding protein NOB1 / PIN domain of ribonuclease / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / RIO kinase / RIO-like kinase / RIO1 family / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Large family of predicted nucleotide-binding domains / Leucine rich repeat 4 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Leucine Rich repeats (2 copies) / PIN domain / Leucine-rich repeats, bacterial type / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / Ribosomal protein S21e / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Leucine rich repeat / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / : / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e 類似検索 - ドメイン・相同性
Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 ...Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Leucine-rich repeat-containing protein 47 / Probable RNA-binding protein EIF1AD / Serine/threonine-protein kinase RIO1 / RNA-binding protein NOB1 類似検索 - 構成要素
ジャーナル: Nature / 年: 2020 タイトル: Structural basis for the final steps of human 40S ribosome maturation. 著者: Michael Ameismeier / Ivo Zemp / Jasmin van den Heuvel / Matthias Thoms / Otto Berninghausen / Ulrike Kutay / Roland Beckmann / 要旨: Eukaryotic ribosomes consist of a small 40S and a large 60S subunit that are assembled in a highly coordinated manner. More than 200 factors ensure correct modification, processing and folding of ...Eukaryotic ribosomes consist of a small 40S and a large 60S subunit that are assembled in a highly coordinated manner. More than 200 factors ensure correct modification, processing and folding of ribosomal RNA and the timely incorporation of ribosomal proteins. Small subunit maturation ends in the cytosol, when the final rRNA precursor, 18S-E, is cleaved at site 3 by the endonuclease NOB1. Previous structures of human 40S precursors have shown that NOB1 is kept in an inactive state by its partner PNO1. The final maturation events, including the activation of NOB1 for the decisive rRNA-cleavage step and the mechanisms driving the dissociation of the last biogenesis factors have, however, remained unresolved. Here we report five cryo-electron microscopy structures of human 40S subunit precursors, which describe the compositional and conformational progression during the final steps of 40S assembly. Our structures explain the central role of RIOK1 in the displacement and dissociation of PNO1, which in turn allows conformational changes and activation of the endonuclease NOB1. In addition, we observe two factors, eukaryotic translation initiation factor 1A domain-containing protein (EIF1AD) and leucine-rich repeat-containing protein 47 (LRRC47), which bind to late pre-40S particles near RIOK1 and the central rRNA helix 44. Finally, functional data shows that EIF1AD is required for efficient assembly factor recycling and 18S-E processing. Our results thus enable a detailed understanding of the last steps in 40S formation in human cells and, in addition, provide evidence for principal differences in small ribosomal subunit formation between humans and the model organism Saccharomyces cerevisiae.
全体 : Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
全体
名称: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
要素
複合体: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
RNA: pre-18S ribosomal RNA
タンパク質・ペプチド: 40S ribosomal protein SA
タンパク質・ペプチド: 40S ribosomal protein S3a
タンパク質・ペプチド: 40S ribosomal protein S2
タンパク質・ペプチド: 40S ribosomal protein S4, X isoform
タンパク質・ペプチド: 40S ribosomal protein S3
タンパク質・ペプチド: 40S ribosomal protein S6
タンパク質・ペプチド: 40S ribosomal protein S7
タンパク質・ペプチド: 40S ribosomal protein S8
タンパク質・ペプチド: 40S ribosomal protein S9
タンパク質・ペプチド: 40S ribosomal protein S5
タンパク質・ペプチド: 40S ribosomal protein S11
タンパク質・ペプチド: 40S ribosomal protein S10
タンパク質・ペプチド: 40S ribosomal protein S13
タンパク質・ペプチド: 40S ribosomal protein S14
タンパク質・ペプチド: 40S ribosomal protein S12
タンパク質・ペプチド: 40S ribosomal protein S15
タンパク質・ペプチド: 40S ribosomal protein S17
タンパク質・ペプチド: 40S ribosomal protein S16
タンパク質・ペプチド: 40S ribosomal protein S18
タンパク質・ペプチド: 40S ribosomal protein S19
タンパク質・ペプチド: 40S ribosomal protein S21
タンパク質・ペプチド: 40S ribosomal protein S15a
タンパク質・ペプチド: 40S ribosomal protein S23
タンパク質・ペプチド: 40S ribosomal protein S24
タンパク質・ペプチド: 40S ribosomal protein S20
タンパク質・ペプチド: 40S ribosomal protein S25
タンパク質・ペプチド: 40S ribosomal protein S27
タンパク質・ペプチド: 40S ribosomal protein S28
タンパク質・ペプチド: 40S ribosomal protein S29
タンパク質・ペプチド: 40S ribosomal protein S30
タンパク質・ペプチド: Ubiquitin-40S ribosomal protein S27a
タンパク質・ペプチド: Receptor of activated protein C kinase 1
タンパク質・ペプチド: Probable RNA-binding protein EIF1AD
タンパク質・ペプチド: Serine/threonine-protein kinase RIO1
タンパク質・ペプチド: RNA-binding protein NOB1
タンパク質・ペプチド: Leucine-rich repeat-containing protein 47
リガンド: ZINC ION
リガンド: MAGNESIUM ION
リガンド: ADENOSINE-5'-TRIPHOSPHATE
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超分子 #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
超分子
名称: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#37 / 詳細: Map filtered at local resolution