+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24422 | |||||||||
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Title | Ytm1 associated nascent 60S in fkbp39 deletion cells class 2 | |||||||||
Map data | Ytm1 associated nascent 60S in fkbp39 deletion cells class 2 | |||||||||
Sample |
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Function / homology | Function and homology information Antigen processing: Ubiquitination & Proteasome degradation / Noc1p-Noc2p complex / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Noc2p-Noc3p complex ...Antigen processing: Ubiquitination & Proteasome degradation / Noc1p-Noc2p complex / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / PeBoW complex / RNA methylation / rRNA base methylation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / nuclear-transcribed mRNA catabolic process / maturation of 5.8S rRNA / cell division site / ribosomal subunit export from nucleus / ribosomal large subunit binding / protein-RNA complex assembly / 90S preribosome / preribosome, large subunit precursor / DNA replication initiation / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA / translation initiation factor activity / ribosome assembly / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / mitotic spindle / rRNA processing / protein transport / ribosome biogenesis / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / RNA helicase activity / rRNA binding / ribosome / structural constituent of ribosome / RNA helicase / translation / mRNA binding / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Bilokapic S / Halic M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Chromatin localization of nucleophosmin organizes ribosome biogenesis. Authors: Ilaria Ugolini / Silvija Bilokapic / Mylene Ferrolino / Josiah Teague / Yinxia Yan / Xuelin Zhou / Ashish Deshmukh / Michael White / Richard W Kriwacki / Mario Halic / Abstract: Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin ...Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24422.map.gz | 269.8 MB | EMDB map data format | |
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Header (meta data) | emd-24422-v30.xml emd-24422.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_24422.png | 46.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24422 | HTTPS FTP |
-Related structure data
Related structure data | 8esrMC 8esqC 8etcC 8etgC 8ethC 8etiC 8etjC 8eugC 8euiC 8eupC 8euyC 8ev3C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24422.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Ytm1 associated nascent 60S in fkbp39 deletion cells class 2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : nascent 60S
Entire | Name: nascent 60S |
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Components |
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-Supramolecule #1: nascent 60S
Supramolecule | Name: nascent 60S / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109000 |