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Yorodumi- EMDB-4350: Cryo-EM structure of a late human pre-40S ribosomal subunit - State D -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4350 | |||||||||||||||
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Title | Cryo-EM structure of a late human pre-40S ribosomal subunit - State D | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | 40S / pre-40S / ribosome biogenesis / RIBOSOME | |||||||||||||||
Function / homology | Function and homology information positive regulation of ribosomal small subunit export from nucleus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response ...positive regulation of ribosomal small subunit export from nucleus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / 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 / regulation of mitotic metaphase/anaphase transition / 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 / U3 snoRNA binding / 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 / preribosome, small subunit precursor / pigmentation / 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 / spindle assembly / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of translational fidelity / 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 | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Ameismeier M / Cheng J | |||||||||||||||
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_4350.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-4350-v30.xml emd-4350.xml | 49.6 KB 49.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4350_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_4350.png | 152.9 KB | ||
Filedesc metadata | emd-4350.cif.gz | 12 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4350 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4350 | HTTPS FTP |
-Validation report
Summary document | emd_4350_validation.pdf.gz | 258.9 KB | Display | EMDB validaton report |
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Full document | emd_4350_full_validation.pdf.gz | 258 KB | Display | |
Data in XML | emd_4350_validation.xml.gz | 13.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4350 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4350 | HTTPS FTP |
-Related structure data
Related structure data | 6g51MC 4337C 4348C 4349C 4351C 4352C 4353C 6g18C 6g4sC 6g4wC 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_4350.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
-Sample components
+Entire : Cryo-EM structure of a late human pre-40S ribosomal subunit - State D
+Supramolecule #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State D
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein S17
+Macromolecule #3: 40S ribosomal protein SA
+Macromolecule #4: 40S ribosomal protein S3a
+Macromolecule #5: 40S ribosomal protein S2
+Macromolecule #6: 40S ribosomal protein S4, X isoform
+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 S11
+Macromolecule #12: 40S ribosomal protein S13
+Macromolecule #13: 40S ribosomal protein S14
+Macromolecule #14: 40S ribosomal protein S21
+Macromolecule #15: 40S ribosomal protein S15a
+Macromolecule #16: 40S ribosomal protein S23
+Macromolecule #17: 40S ribosomal protein S24
+Macromolecule #18: 40S ribosomal protein S27
+Macromolecule #19: 40S ribosomal protein S30
+Macromolecule #20: RNA-binding protein PNO1
+Macromolecule #21: RNA-binding protein NOB1
+Macromolecule #22: Pre-rRNA-processing protein TSR1 homolog
+Macromolecule #23: Serine/threonine-protein kinase RIO2
+Macromolecule #24: Protein LTV1 homolog
+Macromolecule #25: 40S ribosomal protein S29
+Macromolecule #26: 40S ribosomal protein S3
+Macromolecule #27: 40S ribosomal protein S5
+Macromolecule #28: 40S ribosomal protein S10
+Macromolecule #29: 40S ribosomal protein S12
+Macromolecule #30: 40S ribosomal protein S15
+Macromolecule #31: 40S ribosomal protein S16
+Macromolecule #32: 40S ribosomal protein S18
+Macromolecule #33: 40S ribosomal protein S19
+Macromolecule #34: 40S ribosomal protein S20
+Macromolecule #35: 40S ribosomal protein S25
+Macromolecule #36: 40S ribosomal protein S28
+Macromolecule #37: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #38: Receptor of activated protein C kinase 1
-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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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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |