+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35375 | |||||||||
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Title | human nuclear pre-60S ribosomal particle - State E | |||||||||
Map data | human nuclear pre-60S ribosomal particle - State E - post processed | |||||||||
Sample |
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Keywords | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
Function / homology | Function and homology information negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / TORC2 complex binding / GAIT complex / middle ear morphogenesis / regulation of glycolytic process / maturation of 5.8S rRNA / A band / regulation of reactive oxygen species metabolic process / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / 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 / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of cell-cell adhesion / positive regulation of dendritic spine development / homeostatic process / G1 to G0 transition / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / preribosome, large subunit precursor / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / nuclear-transcribed mRNA catabolic process / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / 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) / 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 / protein targeting / protein-RNA complex assembly / cellular response to interleukin-4 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / embryo implantation / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / cytosolic ribosome assembly / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / innate immune response in mucosa / skeletal system development / positive regulation of translation / mRNA 3'-UTR binding / sensory perception of sound / response to insulin / bone development / cellular response to gamma radiation / cellular response to type II interferon / mRNA 5'-UTR binding / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / osteoblast differentiation / cellular response to UV / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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_35375.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-35375-v30.xml emd-35375.xml | 66.4 KB 66.4 KB | Display Display | EMDB header |
Images | emd_35375.png | 155 KB | ||
Filedesc metadata | emd-35375.cif.gz | 15.7 KB | ||
Others | emd_35375_half_map_1.map.gz emd_35375_half_map_2.map.gz | 194.5 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35375 | HTTPS FTP |
-Validation report
Summary document | emd_35375_validation.pdf.gz | 826.6 KB | Display | EMDB validaton report |
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Full document | emd_35375_full_validation.pdf.gz | 826.2 KB | Display | |
Data in XML | emd_35375_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_35375_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35375 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35375 | HTTPS FTP |
-Related structure data
Related structure data | 8ie3MC 8idtC 8idyC 8ineC 8infC 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_35375.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 E - post processed | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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 E - half1
File | emd_35375_half_map_1.map | ||||||||||||
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Annotation | human nuclear pre-60S ribosomal particle - State E - half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: human nuclear pre-60S ribosomal particle - State E - half2
File | emd_35375_half_map_2.map | ||||||||||||
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Annotation | human nuclear pre-60S ribosomal particle - State E - 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: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #41: 28S rRNA
+Macromolecule #2: Eukaryotic translation initiation factor 6
+Macromolecule #3: Probable ribosome biogenesis protein RLP24
+Macromolecule #5: Zinc finger protein 593
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L29
+Macromolecule #8: 60S ribosomal protein L4
+Macromolecule #9: 60S ribosomal protein L30
+Macromolecule #10: 60S ribosomal protein L34
+Macromolecule #11: 60S ribosomal protein L7a
+Macromolecule #12: 60S ribosomal protein L35
+Macromolecule #13: 60S ribosomal protein L9
+Macromolecule #14: 60S ribosomal protein L36
+Macromolecule #15: 60S ribosomal protein L27a
+Macromolecule #16: 60S ribosomal protein L37
+Macromolecule #17: 60S ribosomal protein L38
+Macromolecule #18: 60S ribosomal protein L39
+Macromolecule #19: 60S ribosomal protein L13
+Macromolecule #20: 60S ribosomal protein L14
+Macromolecule #21: 60S ribosomal protein L15
+Macromolecule #22: 60S ribosomal protein L13a
+Macromolecule #23: 60S ribosomal protein L37a
+Macromolecule #24: 60S ribosomal protein L18
+Macromolecule #25: 60S ribosomal protein L19
+Macromolecule #26: 60S ribosomal protein L18a
+Macromolecule #27: 60S ribosomal protein L21
+Macromolecule #28: 60S ribosomal protein L23
+Macromolecule #29: 60S ribosomal protein L23a
+Macromolecule #30: 60S ribosomal protein L26
+Macromolecule #31: 60S ribosomal protein L27
+Macromolecule #32: 60S ribosomal protein L28
+Macromolecule #33: 60S ribosomal protein L8
+Macromolecule #34: 60S ribosomal protein L35a
+Macromolecule #35: 60S ribosomal protein L6
+Macromolecule #36: 60S ribosomal protein L7
+Macromolecule #37: Protein LLP homolog
+Macromolecule #38: G Protein Nucleolar 2
+Macromolecule #39: GTP-binding protein 4
+Macromolecule #40: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #42: 60S ribosomal protein L5
+Macromolecule #43: 60S ribosomal protein L22
+Macromolecule #44: 60S ribosomal protein L31
+Macromolecule #45: 60S ribosomal protein L32
+Macromolecule #46: 60S ribosomal protein L17
+Macromolecule #47: mRNA turnover protein 4 homolog
+Macromolecule #48: 60S ribosomal protein L11
-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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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.8 e/Å2 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34292 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |