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- EMDB-24421: Ytm1 associated nascent 60S in fkbp39 deletion cells class 1B -

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Basic information

Entry
Database: EMDB / ID: EMD-24421
TitleYtm1 associated nascent 60S in fkbp39 deletion cells class 1B
Map dataYtm1 associated nascent 60S in fkbp39 deletion cells class 1B
Sample
  • Complex: nascent 60S
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / cytosolic large ribosomal subunit assembly / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / PeBoW complex ...Major pathway of rRNA processing in the nucleolus and cytosol / cytosolic large ribosomal subunit assembly / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / PeBoW complex / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / maturation of 5.8S rRNA / cell division site / ribosomal large subunit binding / preribosome, large subunit precursor / ribosomal subunit export from nucleus / maturation of LSU-rRNA / ribonucleoprotein complex binding / translation initiation factor activity / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / mitotic spindle / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / hydrolase activity / RNA helicase activity / negative regulation of translation / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 ...WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / U3 snoRNP protein/Ribosome production factor 1 / Pescadillo / Pescadillo N-terminus / Ribosomal biogenesis NSA2 family / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Brix domain / Brix domain / Brix domain profile. / Brix / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / GTP binding domain / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / breast cancer carboxy-terminal domain / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / BRCT domain profile. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L36e signature. / BRCT domain / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L6e / Ribosomal protein L18e / 60S ribosomal protein L6E / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / BRCT domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal protein L15e, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein eL8 / Probable rRNA-processing protein ebp2 / Brix domain-containing protein C4F8.04 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL13B / Pescadillo homolog / Large ribosomal subunit protein eL13 / Ribosome biogenesis protein erb1 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein uL29 ...Large ribosomal subunit protein eL8 / Probable rRNA-processing protein ebp2 / Brix domain-containing protein C4F8.04 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL13B / Pescadillo homolog / Large ribosomal subunit protein eL13 / Ribosome biogenesis protein erb1 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein uL29 / Uncharacterized RNA-binding protein C1827.05c / Large ribosomal subunit protein eL14 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL36B / Probable nucleolar GTP-binding protein 1 / Ribosome biogenesis protein nsa1 / Large ribosomal subunit protein eL37B / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL30B / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL6A / Ribosome biogenesis protein rlp24 / Ribosome biogenesis protein brx1 / Large ribosomal subunit protein uL4B / Large ribosomal subunit protein eL33B / Putative ribosome biogenesis protein C8F11.04 / Protein mak16 / Ribosome biogenesis protein nsa2 / Ribosomal RNA-processing protein 1 homolog / Nucleolar protein 16 / ATP-dependent RNA helicase / Ribosomal protein L26
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBilokapic S / Halic M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141694 United States
CitationJournal: 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
DepositionJul 9, 2021-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24421.png

Downloads & links

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Map

FileDownload / File: emd_24421.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYtm1 associated nascent 60S in fkbp39 deletion cells class 1B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.33652234 - 0.75550884
Average (Standard dev.)0.00035358232 (±0.009787339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : nascent 60S

EntireName: nascent 60S
Components
  • Complex: nascent 60S

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Supramolecule #1: nascent 60S

SupramoleculeName: nascent 60S / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 250000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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