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Yorodumi- EMDB-29265: Human nuclear pre-60S ribosomal subunit (State I1) - Composite map -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29265 | |||||||||
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Title | Human nuclear pre-60S ribosomal subunit (State I1) - 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 : / Las1 complex / protein localization to nucleoplasm / inner cell mass cell differentiation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding ...: / Las1 complex / protein localization to nucleoplasm / inner cell mass cell differentiation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / dynein axonemal particle / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / PTK6 Expression / PeBoW complex / regulation of megakaryocyte differentiation / SUMO binding / positive regulation of protein sumoylation / stem cell division / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / eukaryotic 80S initiation complex / negative regulation of protein neddylation / nuclear pre-replicative complex / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / positive regulation of telomere maintenance / 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 / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of protein K63-linked deubiquitination / 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) / middle ear morphogenesis / nuclear-transcribed mRNA catabolic process / skeletal system morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / positive regulation of signal transduction by p53 class mediator / regulation of reactive oxygen species metabolic process / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / positive regulation of dendritic spine development / negative regulation of ubiquitin protein ligase activity / regulation of glycolytic process / regulation of aerobic respiration / maturation of 5.8S rRNA / rRNA metabolic process / response to aldosterone / stem cell population maintenance / 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 / mitotic G2 DNA damage checkpoint signaling / protein-RNA complex assembly / MLL1 complex / 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 / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to actinomycin D / negative regulation of mitotic cell cycle / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit export from nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / rough endoplasmic reticulum / MDM2/MDM4 family protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 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_29265.map.gz | 133.8 MB | EMDB map data format | |
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Header (meta data) | emd-29265-v30.xml emd-29265.xml | 94.1 KB 94.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29265_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_29265.png | 170.6 KB | ||
Masks | emd_29265_msk_1.map | 421.9 MB | Mask map | |
Others | emd_29265_half_map_1.map.gz emd_29265_half_map_2.map.gz | 391.2 MB 391.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29265 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29265 | HTTPS FTP |
-Related structure data
Related structure data | 8fl2MC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl0C 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_29265.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_29265_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29265_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29265_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human nuclear pre-60S ribosomal subunit (State I1)
+Supramolecule #1: Human nuclear pre-60S ribosomal subunit (State I1)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #2: 60S ribosomal protein L10a
+Macromolecule #3: Ribosomal biogenesis protein LAS1L
+Macromolecule #8: 60S ribosomal protein L11
+Macromolecule #9: 60S ribosomal protein L13
+Macromolecule #10: 60S ribosomal protein L13a
+Macromolecule #11: 60S ribosomal protein L14
+Macromolecule #12: 60S ribosomal protein L15
+Macromolecule #13: 60S ribosomal protein L17
+Macromolecule #14: 60S ribosomal protein L18
+Macromolecule #15: 60S ribosomal protein L18a
+Macromolecule #16: 60S ribosomal protein L19
+Macromolecule #17: 60S ribosomal protein L21
+Macromolecule #18: 60S ribosomal protein L22
+Macromolecule #19: 60S ribosomal protein L23
+Macromolecule #20: 60S ribosomal protein L23a
+Macromolecule #21: 60S ribosomal protein L26
+Macromolecule #22: 60S ribosomal protein L27
+Macromolecule #23: 60S ribosomal protein L27a
+Macromolecule #24: 60S ribosomal protein L28
+Macromolecule #25: 60S ribosomal protein L3
+Macromolecule #26: 60S ribosomal protein L30
+Macromolecule #27: 60S ribosomal protein L31
+Macromolecule #28: 60S ribosomal protein L32
+Macromolecule #29: 60S ribosomal protein L34
+Macromolecule #30: 60S ribosomal protein L35
+Macromolecule #31: 60S ribosomal protein L35a
+Macromolecule #32: 60S ribosomal protein L36
+Macromolecule #33: 60S ribosomal protein L37
+Macromolecule #34: 60S ribosomal protein L37a
+Macromolecule #35: 60S ribosomal protein L38
+Macromolecule #36: 60S ribosomal protein L39
+Macromolecule #37: Guanine nucleotide-binding protein-like 3
+Macromolecule #38: Nucleolar GTP-binding protein 2
+Macromolecule #39: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #40: Notchless protein homolog 1
+Macromolecule #41: Protein LLP homolog
+Macromolecule #42: Ribosome biogenesis protein NOP53
+Macromolecule #43: Zinc finger protein 593
+Macromolecule #44: Protein SDA1 homolog
+Macromolecule #45: Testis-expressed protein 10
+Macromolecule #46: WD repeat-containing protein 18
+Macromolecule #47: Proline-, glutamic acid- and leucine-rich protein 1
+Macromolecule #48: Coiled-coil domain-containing protein 86
+Macromolecule #49: 60S ribosomal protein L4
+Macromolecule #50: 60S ribosomal protein L5
+Macromolecule #51: 60S ribosomal protein L6
+Macromolecule #52: 60S ribosomal protein L7
+Macromolecule #53: 60S ribosomal protein L7a
+Macromolecule #54: 60S ribosomal protein L8
+Macromolecule #55: 60S ribosomal protein L9
+Macromolecule #56: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #57: 60S ribosomal protein L7-like 1
+Macromolecule #58: Eukaryotic translation initiation factor 6
+Macromolecule #59: Ribosomal L1 domain-containing protein 1
+Macromolecule #60: Pescadillo homolog
+Macromolecule #61: mRNA turnover protein 4 homolog
+Macromolecule #62: GTP-binding protein 4
+Macromolecule #63: Probable ribosome biogenesis protein RLP24
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: ITS2 rRNA
+Macromolecule #6: 28S rRNA
+Macromolecule #7: 5S rRNA
+Macromolecule #64: MAGNESIUM ION
+Macromolecule #65: ZINC ION
+Macromolecule #66: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #67: POTASSIUM ION
+Macromolecule #68: GUANOSINE-5'-DIPHOSPHATE
-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-8fl2: |