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Yorodumi- EMDB-29255: Human nucleolar pre-60S ribosomal subunit (State B2) - Composite map -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29255 | |||||||||
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Title | Human nucleolar pre-60S ribosomal subunit (State B2) - Composite map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
Function / homology | Function and homology information RNA 2'-O-methyltransferase activity / granular component / rRNA (uridine-2'-O-)-methyltransferase activity / negative regulation of collagen binding / rRNA (guanine) methyltransferase activity / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / PeBoW complex ...RNA 2'-O-methyltransferase activity / granular component / rRNA (uridine-2'-O-)-methyltransferase activity / negative regulation of collagen binding / rRNA (guanine) methyltransferase activity / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / PeBoW complex / regulation of megakaryocyte differentiation / RNA methylation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / blastocyst formation / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / TORC2 complex binding / protein localization to nucleolus / GAIT complex / G1 to G0 transition / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / nuclear-transcribed mRNA catabolic process / A band / positive regulation of signal transduction by p53 class mediator / regulation of reactive oxygen species metabolic process / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin protein ligase activity / regulation of glycolytic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / maturation of 5.8S rRNA / mitotic metaphase chromosome alignment / rRNA metabolic process / homeostatic process / lung morphogenesis / macrophage chemotaxis / negative regulation of DNA replication / negative regulation of cell-cell adhesion / ribosomal subunit export from nucleus / Protein hydroxylation / 90S preribosome / regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / rRNA transcription / Eukaryotic Translation Termination / preribosome, large subunit precursor / blastocyst development / 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) / cellular response to actinomycin D / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / hematopoietic progenitor cell differentiation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / negative regulation of protein ubiquitination / Transferases; Transferring one-carbon groups; Methyltransferases / translation initiation factor activity / cellular response to interleukin-4 / nuclear periphery / assembly of large subunit precursor of preribosome / cytosolic ribosome / negative regulation of cell migration / cytosolic ribosome assembly / positive regulation of translation / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / mRNA 3'-UTR binding / response to insulin / cellular response to gamma radiation / mRNA 5'-UTR binding / bone development / ribosomal small subunit biogenesis / ribosomal large subunit assembly / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / rRNA processing / osteoblast differentiation / Regulation of expression of SLITs and ROBOs Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Vanden Broeck A / Klinge S | |||||||||
Funding support | European Union, United States, 2 items
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Citation | Journal: Science / Year: 2023 Title: Principles of human pre-60 biogenesis. Authors: Arnaud Vanden Broeck / Sebastian Klinge / Abstract: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29255.map.gz | 56 MB | EMDB map data format | |
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Header (meta data) | emd-29255-v30.xml emd-29255.xml | 77.2 KB 77.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29255_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_29255.png | 143.8 KB | ||
Masks | emd_29255_msk_1.map | 421.9 MB | Mask map | |
Others | emd_29255_half_map_1.map.gz emd_29255_half_map_2.map.gz | 391 MB 391 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29255 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29255 | HTTPS FTP |
-Related structure data
Related structure data | 8fksMC 8fkqC 8fkrC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl0C 8fl2C 8fl3C 8fl4C 8fl6C 8fl7C 8fl9C 8flaC 8flbC 8flcC 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_29255.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.072 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29255_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29255_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29255_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human nucleolar pre-60S ribosomal subunit (State B2)
+Supramolecule #1: Human nucleolar pre-60S ribosomal subunit (State B2)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #5: 60S ribosomal protein L13
+Macromolecule #6: 60S ribosomal protein L13a
+Macromolecule #7: 60S ribosomal protein L14
+Macromolecule #8: 60S ribosomal protein L15
+Macromolecule #9: 60S ribosomal protein L17
+Macromolecule #10: 60S ribosomal protein L18
+Macromolecule #11: 60S ribosomal protein L18a
+Macromolecule #12: 60S ribosomal protein L21
+Macromolecule #13: 60S ribosomal protein L23
+Macromolecule #14: 60S ribosomal protein L23a
+Macromolecule #15: 60S ribosomal protein L26
+Macromolecule #16: 60S ribosomal protein L27a
+Macromolecule #17: 60S ribosomal protein L28
+Macromolecule #18: 60S ribosomal protein L3
+Macromolecule #19: 60S ribosomal protein L32
+Macromolecule #20: 60S ribosomal protein L35
+Macromolecule #21: 60S ribosomal protein L35a
+Macromolecule #22: 60S ribosomal protein L36
+Macromolecule #23: 60S ribosomal protein L37
+Macromolecule #24: Surfeit locus protein 6
+Macromolecule #25: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #26: RRP15-like protein
+Macromolecule #27: Suppressor of SWI4 1 homolog
+Macromolecule #28: 60S ribosomal protein L4
+Macromolecule #29: 60S ribosomal protein L6
+Macromolecule #30: 60S ribosomal protein L7
+Macromolecule #31: 60S ribosomal protein L7a
+Macromolecule #32: 60S ribosomal protein L9
+Macromolecule #33: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #34: 60S ribosomal protein L7-like 1
+Macromolecule #35: pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
+Macromolecule #36: Eukaryotic translation initiation factor 6
+Macromolecule #37: Ribosomal L1 domain-containing protein 1
+Macromolecule #38: Pescadillo homolog
+Macromolecule #39: Probable rRNA-processing protein EBP2
+Macromolecule #40: Ribosome biogenesis protein BRX1 homolog
+Macromolecule #41: mRNA turnover protein 4 homolog
+Macromolecule #42: GTP-binding protein 4
+Macromolecule #43: Ribosome biogenesis protein BOP1
+Macromolecule #44: Ribosome biogenesis regulatory protein homolog
+Macromolecule #45: Probable ribosome biogenesis protein RLP24
+Macromolecule #46: ATP-dependent RNA helicase DDX18
+Macromolecule #47: Nucleolar protein 16
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: ITS2 rRNA
+Macromolecule #4: 28S rRNA
+Macromolecule #48: MAGNESIUM ION
+Macromolecule #49: ZINC ION
+Macromolecule #50: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #51: POTASSIUM 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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Grid | Model: Quantifoil R3.5/1 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV Details: Four applications with manual blotting before last blotting with the vitrobot.. |
-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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 172699 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8fks: |