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- EMDB-14317: Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map -
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Open data
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Basic information
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Title | Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map | |||||||||||||||
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![]() | Ribosome / rRNA modifications / post-translational modifications / cryo-EM | |||||||||||||||
Function / homology | ![]() 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 ...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 / 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 / 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of GTPase activity / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex Similarity search - Function | |||||||||||||||
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Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||||||||
![]() | Pellegrino S / Dent KC / Spikes T / Warren AJ | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution. Authors: Simone Pellegrino / Kyle C Dent / Tobias Spikes / Alan J Warren / ![]() Abstract: The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the ...The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the inability to accurately visualise these modifications has limited mechanistic understanding of the role of these modifications in ribosome function. Here we report the 2.15 Å resolution cryo-EM reconstruction of the human 40S ribosomal subunit. We directly visualise post-transcriptional modifications within the 18S rRNA and four post-translational modifications of ribosomal proteins. Additionally, we interpret the solvation shells in the core regions of the 40S ribosomal subunit and reveal how potassium and magnesium ions establish both universally conserved and eukaryote-specific coordination to promote the stabilisation and folding of key ribosomal elements. This work provides unprecedented structural details for the human 40S ribosomal subunit that will serve as an important reference for unravelling the functional role of ribosomal RNA modifications. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 44.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 48.3 KB 48.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18 KB | Display | ![]() |
Images | ![]() | 59.5 KB | ||
Filedesc metadata | ![]() | 11.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 413.8 KB | Display | ![]() |
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Full document | ![]() | 413.4 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r4xMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8267 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Human 40S ribosomal subunit
+Supramolecule #1: Human 40S ribosomal subunit
+Macromolecule #1: 60S ribosomal protein L41
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: 40S ribosomal protein S3
+Macromolecule #5: 40S ribosomal protein S4, X isoform
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S7
+Macromolecule #8: 40S ribosomal protein S8
+Macromolecule #9: 40S ribosomal protein S10
+Macromolecule #10: 40S ribosomal protein S11
+Macromolecule #11: 40S ribosomal protein S15
+Macromolecule #12: 40S ribosomal protein S16
+Macromolecule #13: 40S ribosomal protein S17
+Macromolecule #14: 40S ribosomal protein S18
+Macromolecule #15: 40S ribosomal protein S19
+Macromolecule #16: 40S ribosomal protein S20
+Macromolecule #17: 40S ribosomal protein S21
+Macromolecule #18: 40S ribosomal protein S23
+Macromolecule #19: 40S ribosomal protein S26
+Macromolecule #20: 40S ribosomal protein S28
+Macromolecule #21: 40S ribosomal protein S29
+Macromolecule #22: 40S ribosomal protein S2
+Macromolecule #23: 40S ribosomal protein S6
+Macromolecule #24: 40S ribosomal protein S9
+Macromolecule #25: 40S ribosomal protein S12
+Macromolecule #26: 40S ribosomal protein S13
+Macromolecule #27: 40S ribosomal protein S14
+Macromolecule #28: 40S ribosomal protein S15a
+Macromolecule #29: 40S ribosomal protein S24
+Macromolecule #30: 40S ribosomal protein S25
+Macromolecule #31: 40S ribosomal protein S27
+Macromolecule #32: 40S ribosomal protein S30
+Macromolecule #33: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #34: Receptor of activated protein C kinase 1
+Macromolecule #35: 40S ribosomal protein SA
+Macromolecule #2: 18S ribosomal RNA
+Macromolecule #36: POTASSIUM ION
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ZINC ION
+Macromolecule #39: water
-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: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.56 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |