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Open data
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Basic information
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| Title | human nuclear pre-60S ribosomal particle - State G' | |||||||||
Map data | human nuclear pre-60S ribosomal particle - State G' - post processed | |||||||||
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Keywords | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
| Function / homology | Function and homology informationprotein 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 / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process ...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 / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of G2/M transition of mitotic cell cycle / PeBoW complex / 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 / positive regulation of protein K63-linked deubiquitination / ribosomal protein import into nucleus / blastocyst formation / protein-DNA complex disassembly / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / protein localization to nucleolus / 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 / regulation of reactive oxygen species metabolic process / negative regulation of cell-cell adhesion / regulation of aerobic respiration / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / homeostatic process / negative regulation of DNA replication / rRNA metabolic process / positive regulation of dendritic spine development / macrophage chemotaxis / negative regulation of signal transduction by p53 class mediator / lung morphogenesis / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / regulation of protein phosphorylation / positive regulation of natural killer cell proliferation / Protein hydroxylation / preribosome, large subunit precursor / Peptide chain elongation / nuclear-transcribed mRNA catabolic process / rRNA transcription / 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 / 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 / ribonucleoprotein complex binding / protein targeting / negative regulation of protein-containing complex assembly / 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 / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 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_35596.map.gz | 12.4 MB | EMDB map data format | |
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| Header (meta data) | emd-35596-v30.xml emd-35596.xml | 81.3 KB 81.3 KB | Display Display | EMDB header |
| Images | emd_35596.png | 171.9 KB | ||
| Filedesc metadata | emd-35596.cif.gz | 18.9 KB | ||
| Others | emd_35596_half_map_1.map.gz emd_35596_half_map_2.map.gz | 194.5 MB 194.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35596 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35596 | HTTPS FTP |
-Validation report
| Summary document | emd_35596_validation.pdf.gz | 858.8 KB | Display | EMDB validaton report |
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| Full document | emd_35596_full_validation.pdf.gz | 858.3 KB | Display | |
| Data in XML | emd_35596_validation.xml.gz | 15.6 KB | Display | |
| Data in CIF | emd_35596_validation.cif.gz | 18.8 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35596 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35596 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8ineMC ![]() 8idtC ![]() 8idyC ![]() 8ie3C ![]() 8infC ![]() 8inkC ![]() 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_35596.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 G' - 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 G' - half1
| File | emd_35596_half_map_1.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - State G' - half1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: human nuclear pre-60S ribosomal particle - State G' - half2
| File | emd_35596_half_map_2.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - State G' - half2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : human nuclear pre-60S state G'
+Supramolecule #1: human nuclear pre-60S state G'
+Macromolecule #1: Ribosomal L1 domain-containing protein 1
+Macromolecule #2: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #3: 60S ribosomal protein L7-like 1
+Macromolecule #5: GTP-binding protein 4
+Macromolecule #7: Eukaryotic translation initiation factor 6
+Macromolecule #8: Probable ribosome biogenesis protein RLP24
+Macromolecule #9: Zinc finger protein 593
+Macromolecule #10: 60S ribosomal protein L3
+Macromolecule #11: 60S ribosomal protein L29
+Macromolecule #12: 60S ribosomal protein L4
+Macromolecule #13: 60S ribosomal protein L30
+Macromolecule #14: 60S ribosomal protein L34
+Macromolecule #15: 60S ribosomal protein L7a
+Macromolecule #16: 60S ribosomal protein L35
+Macromolecule #17: 60S ribosomal protein L9
+Macromolecule #18: 60S ribosomal protein L36
+Macromolecule #19: 60S ribosomal protein L27a
+Macromolecule #20: 60S ribosomal protein L37
+Macromolecule #21: 60S ribosomal protein L11
+Macromolecule #22: 60S ribosomal protein L38
+Macromolecule #23: 60S ribosomal protein L39
+Macromolecule #24: 60S ribosomal protein L13
+Macromolecule #25: 60S ribosomal protein L14
+Macromolecule #26: 60S ribosomal protein L15
+Macromolecule #27: 60S ribosomal protein L13a
+Macromolecule #28: 60S ribosomal protein L37a
+Macromolecule #29: 60S ribosomal protein L17
+Macromolecule #30: 60S ribosomal protein L18
+Macromolecule #31: 60S ribosomal protein L19
+Macromolecule #32: 60S ribosomal protein L18a
+Macromolecule #33: 60S ribosomal protein L21
+Macromolecule #34: 60S ribosomal protein L22
+Macromolecule #35: 60S ribosomal protein L23
+Macromolecule #36: 60S ribosomal protein L23a
+Macromolecule #37: 60S ribosomal protein L26
+Macromolecule #38: 60S ribosomal protein L27
+Macromolecule #39: 60S ribosomal protein L31
+Macromolecule #40: 60S ribosomal protein L32
+Macromolecule #41: 60S ribosomal protein L28
+Macromolecule #42: 60S ribosomal protein L8
+Macromolecule #43: 60S ribosomal protein L35a
+Macromolecule #44: 60S ribosomal protein L6
+Macromolecule #45: 60S ribosomal protein L7
+Macromolecule #46: 60S ribosomal protein L5
+Macromolecule #47: Protein LLP homolog
+Macromolecule #48: G Protein Nucleolar 2
+Macromolecule #49: Translation machinery-associated protein 16
+Macromolecule #50: mRNA turnover protein 4 homolog
+Macromolecule #51: 60S ribosomal protein L12
+Macromolecule #52: Pescadillo homolog
+Macromolecule #54: 60S ribosomal protein L36a
+Macromolecule #55: Leydig cell tumor 10 kDa protein homolog
+Macromolecule #56: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #57: Ribosome biogenesis protein NOP53
+Macromolecule #4: 28S rRNA
+Macromolecule #6: 5S rRNA
+Macromolecule #53: 5.8S rRNA
+Macromolecule #58: Internal Transcribed Spacer 2
+Macromolecule #59: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: POTASSIUM 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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Y (Row.)
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Processing
FIELD EMISSION GUN
