+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35597 | |||||||||
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Title | human nuclear pre-60S ribosomal particle - State F' | |||||||||
Map data | human nuclear pre-60S ribosomal particle - State F' - post processed | |||||||||
Sample |
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Keywords | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
Function / homology | Function and homology information protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament ...protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / PeBoW complex / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / eukaryotic 80S initiation complex / negative regulation of protein neddylation / 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 / 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 / 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 / blastocyst formation / positive regulation of protein K63-linked deubiquitination / TORC2 complex binding / protein localization to nucleolus / GAIT complex / G1 to G0 transition / middle ear morphogenesis / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytoplasmic side of rough endoplasmic reticulum membrane / nuclear-transcribed mRNA catabolic process / A band / regulation of reactive oxygen species metabolic process / positive regulation of signal transduction by p53 class mediator / alpha-beta T cell differentiation / ubiquitin ligase inhibitor activity / regulation of glycolytic process / negative regulation of ubiquitin protein ligase activity / response to aldosterone / regulation of aerobic respiration / rRNA metabolic process / maturation of 5.8S rRNA / homeostatic process / positive regulation of dendritic spine development / 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 / Peptide chain elongation / ribosomal large subunit binding / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / protein-RNA complex assembly / rRNA transcription / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit export from nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / protein targeting / Major pathway of rRNA processing in the nucleolus and cytosol / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / 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 / embryo implantation / cellular response to interleukin-4 / translation initiation factor activity / ossification / assembly of large subunit precursor of preribosome / cytosolic ribosome / negative regulation of cell migration Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zhang Y / Gao N | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2023 Title: Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles. Authors: Yunyang Zhang / Xiaomeng Liang / Sha Luo / Yan Chen / Yu Li / Chengying Ma / Ningning Li / Ning Gao / Abstract: Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo ...Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35597.map.gz | 13.1 MB | EMDB map data format | |
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Header (meta data) | emd-35597-v30.xml emd-35597.xml | 82.3 KB 82.3 KB | Display Display | EMDB header |
Images | emd_35597.png | 165.2 KB | ||
Filedesc metadata | emd-35597.cif.gz | 19 KB | ||
Others | emd_35597_half_map_1.map.gz emd_35597_half_map_2.map.gz | 194.5 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35597 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35597 | HTTPS FTP |
-Related structure data
Related structure data | 8infMC 8idtC 8idyC 8ie3C 8ineC 8inkC 8ipdC 8ipxC 8ipyC 8ir1C 8ir3C M: atomic model generated by this map C: citing same article (ref.) |
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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_35597.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | human nuclear pre-60S ribosomal particle - State F' - post processed | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: human nuclear pre-60S ribosomal particle - State F' - half1
File | emd_35597_half_map_1.map | ||||||||||||
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Annotation | human nuclear pre-60S ribosomal particle - State F' - half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: human nuclear pre-60S ribosomal particle - State F' - half2
File | emd_35597_half_map_2.map | ||||||||||||
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Annotation | human nuclear pre-60S ribosomal particle - State F' - half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : cryo-EM structure of human nuclear pre-60S ribosomal particle - S...
+Supramolecule #1: cryo-EM structure of human nuclear pre-60S ribosomal particle - S...
+Macromolecule #1: Ribosomal L1 domain-containing protein 1
+Macromolecule #2: Protein SDA1 homolog
+Macromolecule #3: 60S ribosomal protein L10a
+Macromolecule #4: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #5: 60S ribosomal protein L7-like 1
+Macromolecule #7: GTP-binding protein 4
+Macromolecule #9: Eukaryotic translation initiation factor 6
+Macromolecule #10: Probable ribosome biogenesis protein RLP24
+Macromolecule #11: Zinc finger protein 593
+Macromolecule #12: 60S ribosomal protein L3
+Macromolecule #13: 60S ribosomal protein L29
+Macromolecule #14: 60S ribosomal protein L4
+Macromolecule #15: 60S ribosomal protein L30
+Macromolecule #16: 60S ribosomal protein L34
+Macromolecule #17: 60S ribosomal protein L7a
+Macromolecule #18: 60S ribosomal protein L35
+Macromolecule #19: 60S ribosomal protein L9
+Macromolecule #20: 60S ribosomal protein L36
+Macromolecule #21: 60S ribosomal protein L27a
+Macromolecule #22: 60S ribosomal protein L37
+Macromolecule #23: 60S ribosomal protein L11
+Macromolecule #24: 60S ribosomal protein L38
+Macromolecule #25: 60S ribosomal protein L39
+Macromolecule #26: 60S ribosomal protein L13
+Macromolecule #27: 60S ribosomal protein L14
+Macromolecule #28: 60S ribosomal protein L15
+Macromolecule #29: 60S ribosomal protein L13a
+Macromolecule #30: 60S ribosomal protein L36a
+Macromolecule #31: 60S ribosomal protein L37a
+Macromolecule #32: 60S ribosomal protein L17
+Macromolecule #33: 60S ribosomal protein L18
+Macromolecule #34: 60S ribosomal protein L19
+Macromolecule #35: 60S ribosomal protein L18a
+Macromolecule #36: 60S ribosomal protein L21
+Macromolecule #37: 60S ribosomal protein L22
+Macromolecule #38: 60S ribosomal protein L23
+Macromolecule #39: 60S ribosomal protein L23a
+Macromolecule #40: 60S ribosomal protein L26
+Macromolecule #41: 60S ribosomal protein L27
+Macromolecule #42: 60S ribosomal protein L31
+Macromolecule #43: 60S ribosomal protein L32
+Macromolecule #44: 60S ribosomal protein L28
+Macromolecule #45: 60S ribosomal protein L8
+Macromolecule #46: 60S ribosomal protein L35a
+Macromolecule #47: 60S ribosomal protein L6
+Macromolecule #48: 60S ribosomal protein L7
+Macromolecule #49: 60S ribosomal protein L5
+Macromolecule #50: Protein LLP homolog
+Macromolecule #51: G Protein Nucleolar 2
+Macromolecule #52: Translation machinery-associated protein 16
+Macromolecule #53: mRNA turnover protein 4 homolog
+Macromolecule #54: Leydig cell tumor 10 kDa protein homolog
+Macromolecule #55: 60S ribosomal protein L12
+Macromolecule #56: Pescadillo homolog
+Macromolecule #58: Uncharacterized protein C11orf98
+Macromolecule #59: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #60: Ribosome biogenesis protein NOP53
+Macromolecule #6: 28S rRNA
+Macromolecule #8: 5S rRNA
+Macromolecule #57: 5.8S rRNA
+Macromolecule #61: Internal Transcribed Spacer 2
+Macromolecule #62: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #63: MAGNESIUM ION
+Macromolecule #64: POTASSIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45905 |