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- EMDB-4337: Cryo-EM structure of a late human pre-40S ribosomal subunit - State C -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4337 | |||||||||||||||
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Title | Cryo-EM structure of a late human pre-40S ribosomal subunit - State C | |||||||||||||||
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![]() | 40S / pre-40S / ribosome biogenesis / RIBOSOME | |||||||||||||||
Function / homology | ![]() positive regulation of ribosomal small subunit export from nucleus / regulation of protein localization to nucleolus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of rRNA processing / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex ...positive regulation of ribosomal small subunit export from nucleus / regulation of protein localization to nucleolus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of rRNA processing / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of mitotic metaphase/anaphase transition / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / U3 snoRNA binding / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / negative regulation of phagocytosis / 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 / snoRNA binding / laminin receptor activity / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / pigmentation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of mitochondrial depolarization / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / cellular response to ethanol / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / protein serine/threonine kinase inhibitor activity / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / L13a-mediated translational silencing of Ceruloplasmin expression / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / TICAM1,TRAF6-dependent induction of TAK1 complex / phagocytic cup / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of translational fidelity / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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) / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Protein methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
![]() | Ameismeier M / Cheng J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Visualizing late states of human 40S ribosomal subunit maturation. Authors: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / ![]() Abstract: The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high- ...The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage. | |||||||||||||||
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 | ![]() | 19.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 51.7 KB 51.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 165.3 KB | ||
Filedesc metadata | ![]() | 12.2 KB | ||
Others | ![]() ![]() | 139.8 MB 139.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 369.1 KB | Display | ![]() |
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Full document | ![]() | 368.2 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g18MC ![]() 4348C ![]() 4349C ![]() 4350C ![]() 4351C ![]() 4352C ![]() 4353C ![]() 6g4sC ![]() 6g4wC ![]() 6g51C ![]() 6g53C ![]() 6g5hC ![]() 6g5iC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Half map: #1
File | emd_4337_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4337_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Cryo-EM structure of a human pre-40S ribosomal subunit with bound...
+Supramolecule #1: Cryo-EM structure of a human pre-40S ribosomal subunit with bound...
+Macromolecule #1: pre-18S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein S5
+Macromolecule #3: 40S ribosomal protein S12
+Macromolecule #4: 40S ribosomal protein S15
+Macromolecule #5: 40S ribosomal protein S16
+Macromolecule #6: 40S ribosomal protein S17
+Macromolecule #7: 40S ribosomal protein S18
+Macromolecule #8: 40S ribosomal protein S19
+Macromolecule #9: 40S ribosomal protein S25
+Macromolecule #10: 40S ribosomal protein S28
+Macromolecule #11: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #12: Receptor of activated protein C kinase 1
+Macromolecule #13: 40S ribosomal protein SA
+Macromolecule #14: 40S ribosomal protein S3a
+Macromolecule #15: 40S ribosomal protein S2
+Macromolecule #16: 40S ribosomal protein S4, X isoform
+Macromolecule #17: 40S ribosomal protein S6
+Macromolecule #18: 40S ribosomal protein S7
+Macromolecule #19: 40S ribosomal protein S8
+Macromolecule #20: 40S ribosomal protein S9
+Macromolecule #21: 40S ribosomal protein S11
+Macromolecule #22: 40S ribosomal protein S13
+Macromolecule #23: 40S ribosomal protein S14
+Macromolecule #24: 40S ribosomal protein S21
+Macromolecule #25: 40S ribosomal protein S15a
+Macromolecule #26: 40S ribosomal protein S23
+Macromolecule #27: 40S ribosomal protein S24
+Macromolecule #28: 40S ribosomal protein S27
+Macromolecule #29: 40S ribosomal protein S30
+Macromolecule #30: RNA-binding protein PNO1
+Macromolecule #31: RNA-binding protein NOB1
+Macromolecule #32: Pre-rRNA-processing protein TSR1 homolog
+Macromolecule #33: Bystin
+Macromolecule #34: Serine/threonine-protein kinase RIO2
+Macromolecule #35: Protein LTV1 homolog
+Macromolecule #36: ZINC ION
-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: 2.5 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 |