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- EMDB-11519: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11519 | |||||||||
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Title | Cryo-EM structure of a late human pre-40S ribosomal subunit - State G | |||||||||
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Function / homology | ![]() methyltransferase complex / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / 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 / positive regulation of rRNA processing ...methyltransferase complex / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / 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 / positive regulation of rRNA processing / 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 RNA splicing / negative regulation of DNA repair / 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 / 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 / protein kinase A binding / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / pigmentation / preribosome, small subunit precursor / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / spindle assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytosolic ribosome / positive regulation of cell cycle / signaling adaptor activity / negative regulation of smoothened signaling pathway / stress granule assembly / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / laminin binding / rough endoplasmic reticulum / 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) / EML4 and NUDC in mitotic spindle formation Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Ameismeier M / Zemp I / van den Heuvel J / Thoms M / Berninghausen O / Kutay U / Beckmann R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 104.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 52.2 KB 52.2 KB | Display Display | ![]() |
Images | ![]() | 156.7 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Others | ![]() ![]() ![]() | 166.3 MB 140.8 MB 140.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 399.8 KB | Display | ![]() |
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Full document | ![]() | 398.9 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zxfMC ![]() 6zxdC ![]() 6zxeC ![]() 6zxgC ![]() 6zxhC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: #1
File | emd_11519_additional_1.map | ||||||||||||
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-Half map: #2
File | emd_11519_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_11519_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
+Supramolecule #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State G
+Macromolecule #1: pre-18S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein SA
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: 40S ribosomal protein S2
+Macromolecule #5: 40S ribosomal protein S4, X isoform
+Macromolecule #6: 40S ribosomal protein S3
+Macromolecule #7: 40S ribosomal protein S6
+Macromolecule #8: 40S ribosomal protein S7
+Macromolecule #9: 40S ribosomal protein S8
+Macromolecule #10: 40S ribosomal protein S9
+Macromolecule #11: 40S ribosomal protein S5
+Macromolecule #12: 40S ribosomal protein S11
+Macromolecule #13: 40S ribosomal protein S10
+Macromolecule #14: 40S ribosomal protein S13
+Macromolecule #15: 40S ribosomal protein S14
+Macromolecule #16: 40S ribosomal protein S12
+Macromolecule #17: 40S ribosomal protein S15
+Macromolecule #18: 40S ribosomal protein S17
+Macromolecule #19: 40S ribosomal protein S16
+Macromolecule #20: 40S ribosomal protein S18
+Macromolecule #21: 40S ribosomal protein S19
+Macromolecule #22: 40S ribosomal protein S21
+Macromolecule #23: 40S ribosomal protein S15a
+Macromolecule #24: 40S ribosomal protein S23
+Macromolecule #25: 40S ribosomal protein S24
+Macromolecule #26: 40S ribosomal protein S20
+Macromolecule #27: 40S ribosomal protein S25
+Macromolecule #28: 40S ribosomal protein S27
+Macromolecule #29: 40S ribosomal protein S28
+Macromolecule #30: 40S ribosomal protein S29
+Macromolecule #31: 40S ribosomal protein S30
+Macromolecule #32: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #33: Receptor of activated protein C kinase 1
+Macromolecule #34: Probable RNA-binding protein EIF1AD
+Macromolecule #35: Serine/threonine-protein kinase RIO1
+Macromolecule #36: RNA-binding protein NOB1
+Macromolecule #37: Leucine-rich repeat-containing protein 47
+Macromolecule #38: ZINC ION
+Macromolecule #39: MAGNESIUM ION
+Macromolecule #40: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | #0 - Type of model: PDB ENTRY #0 - PDB model - PDB ID: #1 - Type of model: PDB ENTRY #1 - PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140612 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |