- EMDB-11518: Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2 -
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Basic information
Entry
Database: EMDB / ID: EMD-11518
Title
Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2
Map data
Sample
Complex: Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2
RNA: x 1 types
Protein or peptide: x 36 types
Ligand: x 1 types
Keywords
Ribosome Biogenesis / Pre-40S / RIBOSOME
Function / homology
Function and homology information
methyltransferase complex / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / positive regulation of rRNA processing / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...methyltransferase complex / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / positive regulation of rRNA processing / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / supercoiled DNA binding / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / protein kinase A binding / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / positive regulation of signal transduction by p53 class mediator / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / protein serine/threonine kinase inhibitor activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / phagocytic cup / regulation of translational fidelity / 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) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Protein methylation / spindle assembly / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of intrinsic apoptotic signaling pathway / laminin binding / rough endoplasmic reticulum / translation regulator activity / positive regulation of cell cycle / translation initiation factor binding / gastrulation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of protein binding / signaling adaptor activity / Maturation of protein E / Maturation of protein E / MDM2/MDM4 family protein binding / ER Quality Control Compartment (ERQC) / positive regulation of microtubule polymerization Similarity search - Function
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 ...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. / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/4 domain / RIO kinase / RIO-like kinase / : / RIO domain / : / : / Eukaryotic type KH-domain (KH-domain type I) (327.11.2) / Large family of predicted nucleotide-binding domains / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / PIN domain / Leucine-rich repeats, bacterial type / K Homology domain, type 1 superfamily / 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 S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Leucine rich repeat / S27a-like superfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / 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 S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19A/S15e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region Similarity search - Domain/homology
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 / Serine/threonine-protein kinase RIO1 / RNA-binding protein PNO1 / RNA-binding protein NOB1 Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.0 Å
Journal: Nature / Year: 2020 Title: Structural basis for the final steps of human 40S ribosome maturation. Authors: Michael Ameismeier / Ivo Zemp / Jasmin van den Heuvel / Matthias Thoms / Otto Berninghausen / Ulrike Kutay / Roland Beckmann / Abstract: 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.
History
Deposition
Jul 29, 2020
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Header (metadata) release
Dec 2, 2020
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Map release
Dec 2, 2020
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Update
May 1, 2024
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Current status
May 1, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2
Entire
Name: Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2
Components
Complex: Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2
RNA: pre-18S ribosomal RNA
Protein or peptide: 40S ribosomal protein S17
Protein or peptide: 40S ribosomal protein SA
Protein or peptide: 40S ribosomal protein S3a
Protein or peptide: 40S ribosomal protein S2
Protein or peptide: 40S ribosomal protein S4, X isoform
Protein or peptide: 40S ribosomal protein S6
Protein or peptide: 40S ribosomal protein S7
Protein or peptide: 40S ribosomal protein S8
Protein or peptide: 40S ribosomal protein S9
Protein or peptide: 40S ribosomal protein S11
Protein or peptide: 40S ribosomal protein S13
Protein or peptide: 40S ribosomal protein S14
Protein or peptide: 40S ribosomal protein S21
Protein or peptide: 40S ribosomal protein S15a
Protein or peptide: 40S ribosomal protein S23
Protein or peptide: 40S ribosomal protein S24
Protein or peptide: 40S ribosomal protein S27
Protein or peptide: 40S ribosomal protein S30
Protein or peptide: RNA-binding protein PNO1
Protein or peptide: RNA-binding protein NOB1
Protein or peptide: 40S ribosomal protein S29
Protein or peptide: 40S ribosomal protein S3
Protein or peptide: 40S ribosomal protein S5
Protein or peptide: 40S ribosomal protein S10
Protein or peptide: 40S ribosomal protein S12
Protein or peptide: 40S ribosomal protein S15
Protein or peptide: 40S ribosomal protein S16
Protein or peptide: 40S ribosomal protein S18
Protein or peptide: 40S ribosomal protein S19
Protein or peptide: 40S ribosomal protein S20
Protein or peptide: 40S ribosomal protein S25
Protein or peptide: 40S ribosomal protein S28
Protein or peptide: Ubiquitin-40S ribosomal protein S27a
Protein or peptide: Receptor of activated protein C kinase 1
Protein or peptide: Leucine-rich repeat-containing protein 47
Protein or peptide: Serine/threonine-protein kinase RIO1
Ligand: ZINC ION
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Supramolecule #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2
Supramolecule
Name: Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#37 / Details: Map filtered at local resolution
Source (natural)
Organism: Homo sapiens (human) / Strain: HEK293T
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Macromolecule #1: pre-18S ribosomal RNA
Macromolecule
Name: pre-18S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
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