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Yorodumi- EMDB-11520: Cryo-EM structure of a late human pre-40S ribosomal subunit - State H1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11520 | |||||||||
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Title | Cryo-EM structure of a late human pre-40S ribosomal subunit - State H1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 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 rRNA processing / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nucleolus organization ...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 rRNA processing / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / TNFR1-mediated ceramide production / negative regulation of RNA splicing / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / pigmentation / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / IRE1-RACK1-PP2A complex / ion channel inhibitor activity / positive regulation of Golgi to plasma membrane protein transport / preribosome, small subunit precursor / negative regulation of DNA repair / Translation initiation complex formation / oxidized purine DNA binding / negative regulation of Wnt signaling pathway / supercoiled DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / NF-kappaB complex / negative regulation of phagocytosis / fibroblast growth factor binding / ubiquitin-like protein conjugating enzyme binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / mTORC1-mediated signalling / protein kinase A binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / monocyte chemotaxis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / phagocytic cup / positive regulation of mitochondrial depolarization / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of T cell receptor signaling pathway / Viral mRNA Translation / positive regulation of activated T cell proliferation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of respiratory burst involved in inflammatory response / 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 / BH3 domain 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) / regulation of translational fidelity / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit export from nucleus / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of cell cycle / stress granule assembly / translation initiation factor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / maturation of SSU-rRNA / rough endoplasmic reticulum / laminin binding / Mitotic Prometaphase / gastrulation / spindle assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / positive regulation of apoptotic signaling pathway / Maturation of protein E / positive regulation of JUN kinase activity / Maturation of protein E / ER Quality Control Compartment (ERQC) Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Ameismeier M / Zemp I / van den Heuvel J / Thoms M / Berninghausen O / Kutay U / Beckmann R | |||||||||
Funding support | Germany, 1 items
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Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11520.map.gz | 105.1 MB | EMDB map data format | |
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Header (meta data) | emd-11520-v30.xml emd-11520.xml | 52.4 KB 52.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11520_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_11520.png | 171.2 KB | ||
Masks | emd_11520_msk_1.map | 178 MB | Mask map | |
Others | emd_11520_additional_1.map.gz emd_11520_half_map_1.map.gz emd_11520_half_map_2.map.gz | 166.8 MB 140.8 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11520 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11520 | HTTPS FTP |
-Related structure data
Related structure data | 6zxgMC 6zxdC 6zxeC 6zxfC 6zxhC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11520.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11520_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: postprocessed
File | emd_11520_additional_1.map | ||||||||||||
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Annotation | postprocessed | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_11520_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_11520_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of a late human pre-40S ribosomal subunit - State H1
+Supramolecule #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State H1
+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 S26
+Macromolecule #6: 40S ribosomal protein S4, X isoform
+Macromolecule #7: 40S ribosomal protein S3
+Macromolecule #8: 40S ribosomal protein S6
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: 40S ribosomal protein S8
+Macromolecule #11: 40S ribosomal protein S9
+Macromolecule #12: 40S ribosomal protein S5
+Macromolecule #13: 40S ribosomal protein S11
+Macromolecule #14: 40S ribosomal protein S10
+Macromolecule #15: 40S ribosomal protein S13
+Macromolecule #16: 40S ribosomal protein S14
+Macromolecule #17: 40S ribosomal protein S12
+Macromolecule #18: 40S ribosomal protein S15
+Macromolecule #19: 40S ribosomal protein S17
+Macromolecule #20: 40S ribosomal protein S16
+Macromolecule #21: 40S ribosomal protein S18
+Macromolecule #22: 40S ribosomal protein S19
+Macromolecule #23: 40S ribosomal protein S21
+Macromolecule #24: 40S ribosomal protein S15a
+Macromolecule #25: 40S ribosomal protein S23
+Macromolecule #26: 40S ribosomal protein S24
+Macromolecule #27: 40S ribosomal protein S20
+Macromolecule #28: 40S ribosomal protein S25
+Macromolecule #29: 40S ribosomal protein S27
+Macromolecule #30: 40S ribosomal protein S28
+Macromolecule #31: 40S ribosomal protein S29
+Macromolecule #32: 40S ribosomal protein S30
+Macromolecule #33: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #34: Receptor of activated protein C kinase 1
+Macromolecule #35: Probable RNA-binding protein EIF1AD
+Macromolecule #36: Leucine-rich repeat-containing protein 47
+Macromolecule #37: Serine/threonine-protein kinase RIO1
+Macromolecule #38: MAGNESIUM ION
+Macromolecule #39: ZINC ION
+Macromolecule #40: ASPARTIC ACID
+Macromolecule #41: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |