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Yorodumi- EMDB-4337: Cryo-EM structure of a late human pre-40S ribosomal subunit - State C -
+Open data
-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 | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information 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 / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / 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 / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / laminin receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic metaphase/anaphase transition / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / U3 snoRNA binding / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / preribosome, small subunit precursor / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / snoRNA binding / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / 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) / rough endoplasmic reticulum / regulation of translational fidelity / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / stress granule assembly / translation initiation factor binding / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / RNA endonuclease activity / translational initiation / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Ameismeier M / Cheng J / Berninghausen O / Beckmann R | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: Nature / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4337.map.gz | 19.5 MB | EMDB map data format | |
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Header (meta data) | emd-4337-v30.xml emd-4337.xml | 48.8 KB 48.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4337_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_4337.png | 165.3 KB | ||
Others | emd_4337_half_map_1.map.gz emd_4337_half_map_2.map.gz | 139.8 MB 139.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4337 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4337 | 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 (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_4337.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: 1.084 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 |
-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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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: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |