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Open data
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Basic information
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| Title | human nuclear pre-60S ribosomal particle - State D | |||||||||
Map data | human nuclear pre-60S ribosomal particle - State D - post processed | |||||||||
Sample |
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Keywords | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
| Function / homology | Function and homology informationnegative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / regulation of Notch signaling pathway ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of G2/M transition of mitotic cell cycle / positive regulation of protein sumoylation / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / ribosomal protein import into nucleus / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / negative regulation of mitotic cell cycle / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of glycolytic process / middle ear morphogenesis / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / negative regulation of cell-cell adhesion / cytoplasmic side of rough endoplasmic reticulum membrane / stem cell division / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / stem cell population maintenance / homeostatic process / negative regulation of DNA replication / positive regulation of dendritic spine development / macrophage chemotaxis / lung morphogenesis / positive regulation of telomere maintenance / ribosomal large subunit binding / positive regulation of natural killer cell proliferation / Protein hydroxylation / preribosome, large subunit precursor / Peptide chain elongation / nuclear-transcribed mRNA catabolic process / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / ribosomal large subunit export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of protein binding / Major pathway of rRNA processing in the nucleolus and cytosol / somitogenesis / protein targeting / ribosomal subunit export from nucleus / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / rough endoplasmic reticulum / Notch signaling pathway / MDM2/MDM4 family protein binding / translation initiation factor activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / embryo implantation / cytosolic ribosome / cellular response to interleukin-4 / ossification / negative regulation of cell migration / assembly of large subunit precursor of preribosome / positive regulation of translation / regulation of signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cytosolic ribosome assembly / mRNA 3'-UTR binding / innate immune response in mucosa / skeletal system development / DNA damage response, signal transduction by p53 class mediator / kidney development Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Zhang Y / Gao N | |||||||||
| Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2023Title: 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_35599.map.gz | 9.9 MB | EMDB map data format | |
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| Header (meta data) | emd-35599-v30.xml emd-35599.xml | 76.3 KB 76.3 KB | Display Display | EMDB header |
| Images | emd_35599.png | 161.5 KB | ||
| Filedesc metadata | emd-35599.cif.gz | 18.1 KB | ||
| Others | emd_35599_half_map_1.map.gz emd_35599_half_map_2.map.gz | 194.1 MB 194.6 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35599 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35599 | HTTPS FTP |
-Validation report
| Summary document | emd_35599_validation.pdf.gz | 852.6 KB | Display | EMDB validaton report |
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| Full document | emd_35599_full_validation.pdf.gz | 852.2 KB | Display | |
| Data in XML | emd_35599_validation.xml.gz | 15.6 KB | Display | |
| Data in CIF | emd_35599_validation.cif.gz | 18.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35599 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35599 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8inkMC ![]() 8idtC ![]() 8idyC ![]() 8ie3C ![]() 8ineC ![]() 8infC ![]() 8ipdC ![]() 8ipxC ![]() 8ipyC ![]() 8ir1C ![]() 8ir3C M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_35599.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 D - 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 D - half1
| File | emd_35599_half_map_1.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - State D - half1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: human nuclear pre-60S ribosomal particle - State D - half2
| File | emd_35599_half_map_2.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - State D - half2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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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: Protein SDA1 homolog
+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 L29
+Macromolecule #7: 60S ribosomal protein L3
+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: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #15: 60S ribosomal protein L36
+Macromolecule #16: 60S ribosomal protein L27a
+Macromolecule #17: 60S ribosomal protein L37
+Macromolecule #18: 60S ribosomal protein L38
+Macromolecule #19: 60S ribosomal protein L39
+Macromolecule #20: 60S ribosomal protein L13
+Macromolecule #21: 60S ribosomal protein L14
+Macromolecule #22: 60S ribosomal protein L15
+Macromolecule #23: 60S ribosomal protein L13a
+Macromolecule #24: 60S ribosomal protein L37a
+Macromolecule #25: 60S ribosomal protein L18
+Macromolecule #26: 60S ribosomal protein L19
+Macromolecule #27: 60S ribosomal protein L18a
+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: Coiled-coil domain-containing protein 86
+Macromolecule #38: Guanine nucleotide-binding protein-like 3
+Macromolecule #39: G Protein Nucleolar 2
+Macromolecule #40: 60S ribosomal protein L12
+Macromolecule #41: Protein LLP homolog
+Macromolecule #42: 60S ribosomal protein L11
+Macromolecule #43: 60S ribosomal protein L5
+Macromolecule #44: Notchless protein homolog 1
+Macromolecule #45: 60S ribosomal protein L21
+Macromolecule #46: GTP-binding protein 4
+Macromolecule #47: 60S ribosomal protein L17
+Macromolecule #48: 60S ribosomal protein L32
+Macromolecule #49: 60S ribosomal protein L31
+Macromolecule #50: 60S ribosomal protein L22
+Macromolecule #52: mRNA turnover protein 4 homolog
+Macromolecule #4: 5.8S rRNA
+Macromolecule #51: 5S rRNA
+Macromolecule #53: 28S rRNA
+Macromolecule #54: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: MAGNESIUM ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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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 |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
China, 1 items
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Processing
FIELD EMISSION GUN
