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Yorodumi- EMDB-29252: Human nucleolar pre-60S ribosomal subunit (State A1) - Composite map -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29252 | |||||||||
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Title | Human nucleolar pre-60S ribosomal subunit (State A1) - 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 / positive regulation of protein localization to chromosome, telomeric region / RNA metabolic process / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / preribosome binding / regulation of cellular senescence / lamin filament ...RNA 2'-O-methyltransferase activity / granular component / positive regulation of protein localization to chromosome, telomeric region / RNA metabolic process / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / RNA methylation / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / positive regulation of telomere maintenance / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / rRNA primary transcript binding / blastocyst formation / protein localization to nucleolus / TORC2 complex binding / GAIT complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / regulation of G1 to G0 transition / 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 / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / 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 / mitotic metaphase chromosome alignment / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / G1 to G0 transition / rRNA metabolic process / homeostatic process / negative regulation of cell-cell adhesion / negative regulation of DNA replication / maturation of 5.8S rRNA / lung morphogenesis / Protein hydroxylation / macrophage chemotaxis / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / rRNA transcription / blastocyst development / preribosome, large subunit precursor / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / cellular response to interleukin-4 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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) / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / translation initiation factor activity / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell migration / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / 90S preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / molecular condensate scaffold activity / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / mRNA 3'-UTR binding / positive regulation of translation / response to insulin / bone development / ribosomal large subunit assembly / cellular response to gamma radiation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 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_29252.map.gz | 56.4 MB | EMDB map data format | |
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Header (meta data) | emd-29252-v30.xml emd-29252.xml | 83 KB 83 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29252_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_29252.png | 148.4 KB | ||
Masks | emd_29252_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-29252.cif.gz | 19.6 KB | ||
Others | emd_29252_half_map_1.map.gz emd_29252_half_map_2.map.gz | 391.1 MB 391.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29252 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29252 | HTTPS FTP |
-Validation report
Summary document | emd_29252_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29252_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29252_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | emd_29252_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29252 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29252 | HTTPS FTP |
-Related structure data
Related structure data | 8fkpMC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl0C 8fl2C 8fl3C 8fl4C 8fl6C 8fl7C 8fl9C 8flaC 8flbC 8flcC 8fldC 8fleC 8flfC 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_29252.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_29252_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29252_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29252_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 A1)
+Supramolecule #1: Human nucleolar pre-60S ribosomal subunit (State A1)
+Macromolecule #1: 5.8S rRNA
+Macromolecule #2: ITS2 rRNA
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 60S ribosomal protein L13
+Macromolecule #5: 60S ribosomal protein L13a
+Macromolecule #6: 60S ribosomal protein L14
+Macromolecule #7: 60S ribosomal protein L15
+Macromolecule #8: 60S ribosomal protein L17
+Macromolecule #9: 60S ribosomal protein L18
+Macromolecule #10: 60S ribosomal protein L18a
+Macromolecule #11: 60S ribosomal protein L21
+Macromolecule #12: 60S ribosomal protein L23
+Macromolecule #13: 60S ribosomal protein L23a
+Macromolecule #14: 60S ribosomal protein L26
+Macromolecule #15: 60S ribosomal protein L27a
+Macromolecule #16: 60S ribosomal protein L3
+Macromolecule #17: 60S ribosomal protein L32
+Macromolecule #18: 60S ribosomal protein L35
+Macromolecule #19: 60S ribosomal protein L35a
+Macromolecule #20: 60S ribosomal protein L36
+Macromolecule #21: 60S ribosomal protein L37
+Macromolecule #22: Guanine nucleotide-binding protein-like 3
+Macromolecule #23: Surfeit locus protein 6
+Macromolecule #24: RRP15-like protein
+Macromolecule #25: Protein MAK16 homolog
+Macromolecule #26: Suppressor of SWI4 1 homolog
+Macromolecule #27: Ribosomal RNA processing protein 1 homolog A
+Macromolecule #28: WD repeat-containing protein 74
+Macromolecule #29: Ribosome production factor 1
+Macromolecule #30: 60S ribosomal protein L4
+Macromolecule #31: 60S ribosomal protein L6
+Macromolecule #32: 60S ribosomal protein L7
+Macromolecule #33: 60S ribosomal protein L7a
+Macromolecule #34: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #35: 60S ribosomal protein L7-like 1
+Macromolecule #36: pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
+Macromolecule #37: Eukaryotic translation initiation factor 6
+Macromolecule #38: Ribosomal L1 domain-containing protein 1
+Macromolecule #39: Pescadillo homolog
+Macromolecule #40: Probable rRNA-processing protein EBP2
+Macromolecule #41: Ribosome biogenesis protein BRX1 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 #48: MAGNESIUM ION
+Macromolecule #49: ZINC ION
+Macromolecule #50: IRON/SULFUR CLUSTER
-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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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000 |
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-8fkp: |