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Yorodumi- EMDB-4348: Cryo-EM structure of a late human pre-40S ribosomal subunit - State B -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4348 | |||||||||||||||
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Title | Cryo-EM structure of a late human pre-40S ribosomal subunit - State B | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | 40S / pre-40S / ribosome biogenesis / RIBOSOME | |||||||||||||||
Function / homology | Function and homology information 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 respiratory burst involved in inflammatory response / nucleolus organization / negative regulation of RNA splicing / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis ...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 respiratory burst involved in inflammatory response / nucleolus organization / negative regulation of RNA splicing / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / snoRNA binding / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / fibroblast growth factor binding / monocyte chemotaxis / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of cell cycle / translation regulator activity / stress granule assembly / Mitotic Prometaphase / laminin binding / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / cytosolic ribosome / 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) / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / visual perception / RNA endonuclease activity / erythrocyte differentiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / stem cell proliferation / innate immune response in mucosa / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / neural tube closure / mRNA 3'-UTR binding / small-subunit processome / translational initiation / positive regulation of translation / liver regeneration / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / placenta development / mRNA 5'-UTR binding / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / osteoblast differentiation / G1/S transition of mitotic cell cycle / rRNA processing / Separation of Sister Chromatids / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit rRNA binding / apical part of cell / antibacterial humoral response / ribosome binding / glucose homeostasis Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 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_4348.map.gz | 17.4 MB | EMDB map data format | |
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Header (meta data) | emd-4348-v30.xml emd-4348.xml | 47.8 KB 47.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4348_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_4348.png | 159.9 KB | ||
Filedesc metadata | emd-4348.cif.gz | 11 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4348 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4348 | HTTPS FTP |
-Validation report
Summary document | emd_4348_validation.pdf.gz | 257.2 KB | Display | EMDB validaton report |
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Full document | emd_4348_full_validation.pdf.gz | 256.3 KB | Display | |
Data in XML | emd_4348_validation.xml.gz | 13.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4348 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4348 | HTTPS FTP |
-Related structure data
Related structure data | 6g4sMC 4337C 4349C 4350C 4351C 4352C 4353C 6g18C 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_4348.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
+Entire : Cryo-EM structure of a late human pre-40S ribosomal subunit - State B
+Supramolecule #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State B
+Macromolecule #1: pre-18S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein S17
+Macromolecule #3: 40S ribosomal protein SA
+Macromolecule #4: 40S ribosomal protein S27
+Macromolecule #5: 40S ribosomal protein S3a
+Macromolecule #6: 40S ribosomal protein S2
+Macromolecule #7: 40S ribosomal protein S28
+Macromolecule #8: 40S ribosomal protein S4, X isoform
+Macromolecule #9: 40S ribosomal protein S30
+Macromolecule #10: 40S ribosomal protein S5
+Macromolecule #11: 40S ribosomal protein S7
+Macromolecule #12: 40S ribosomal protein S6
+Macromolecule #13: 40S ribosomal protein S25
+Macromolecule #14: 40S ribosomal protein S24
+Macromolecule #15: RNA-binding protein NOB1
+Macromolecule #16: RNA-binding protein PNO1
+Macromolecule #17: 40S ribosomal protein S23
+Macromolecule #18: Bystin
+Macromolecule #19: 40S ribosomal protein S15a
+Macromolecule #20: 40S ribosomal protein S21
+Macromolecule #21: Pre-rRNA-processing protein TSR1 homolog
+Macromolecule #22: Protein LTV1 homolog
+Macromolecule #23: 40S ribosomal protein S19
+Macromolecule #24: 40S ribosomal protein S18
+Macromolecule #25: 40S ribosomal protein S16
+Macromolecule #26: 40S ribosomal protein S15
+Macromolecule #27: 40S ribosomal protein S14
+Macromolecule #28: 40S ribosomal protein S13
+Macromolecule #29: 40S ribosomal protein S11
+Macromolecule #30: 40S ribosomal protein S9
+Macromolecule #31: 40S ribosomal protein S8
+Macromolecule #32: RRP12
+Macromolecule #33: Unknown
-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 |