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Open data
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Basic information
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| Title | human nuclear pre-60S ribosomal particle - State A | |||||||||
Map data | human nuclear pre-60S ribosomal particle - Stata A - post-precessed | |||||||||
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Keywords | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
| Function / homology | Function and homology informationRNA 2'-O-methyltransferase activity / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / rRNA (uridine-2'-O-)-methyltransferase activity / dendrite extension / rRNA (guanine) methyltransferase activity / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament ...RNA 2'-O-methyltransferase activity / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / rRNA (uridine-2'-O-)-methyltransferase activity / dendrite extension / rRNA (guanine) methyltransferase activity / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / RNA methylation / 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 / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / protein localization to nucleolus / ribosomal protein import into nucleus / negative regulation of mitotic cell cycle / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / rRNA methylation / alpha-beta T cell differentiation / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / regulation of glycolytic process / TORC2 complex binding / G1 to G0 transition / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / negative regulation of cell-cell adhesion / middle ear morphogenesis / maturation of 5.8S rRNA / stem cell division / preribosome, small subunit precursor / mitotic metaphase chromosome alignment / cytoplasmic side of rough endoplasmic reticulum membrane / stem cell population maintenance / negative regulation of ubiquitin protein ligase activity / homeostatic process / negative regulation of DNA replication / positive regulation of dendritic spine development / macrophage chemotaxis / ribosomal large subunit binding / lung morphogenesis / positive regulation of telomere maintenance / positive regulation of natural killer cell proliferation / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to actinomycin D / Eukaryotic Translation Termination / blastocyst development / negative regulation of ubiquitin-dependent protein catabolic process / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / somitogenesis / positive regulation of protein binding / L13a-mediated translational silencing of Ceruloplasmin expression / hematopoietic progenitor cell differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / Notch signaling pathway / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor activity / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / cytosolic ribosome / cellular response to interleukin-4 / ossification / negative regulation of cell migration / Transferases; Transferring one-carbon groups; Methyltransferases / assembly of large subunit precursor of preribosome / regulation of signal transduction by p53 class mediator 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: 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_35672.map.gz | 10 MB | EMDB map data format | |
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| Header (meta data) | emd-35672-v30.xml emd-35672.xml | 76.8 KB 76.8 KB | Display Display | EMDB header |
| Images | emd_35672.png | 148 KB | ||
| Filedesc metadata | emd-35672.cif.gz | 18.4 KB | ||
| Others | emd_35672_half_map_1.map.gz emd_35672_half_map_2.map.gz | 194.3 MB 194.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35672 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35672 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8ir1MC ![]() 8idtC ![]() 8idyC ![]() 8ie3C ![]() 8ineC ![]() 8infC ![]() 8inkC ![]() 8ipdC ![]() 8ipxC ![]() 8ipyC ![]() 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_35672.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 - Stata A - post-precessed | ||||||||||||||||||||||||||||||||||||
| 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 - Stata A - half1
| File | emd_35672_half_map_1.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - Stata A - half1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: human nuclear pre-60S ribosomal particle - Stata A - half2
| File | emd_35672_half_map_2.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - Stata A - 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: 60S ribosomal protein L12
+Macromolecule #2: GTP-binding protein 4
+Macromolecule #3: Eukaryotic translation initiation factor 6
+Macromolecule #4: Probable ribosome biogenesis protein RLP24
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L30
+Macromolecule #8: 60S ribosomal protein L34
+Macromolecule #9: 60S ribosomal protein L7a
+Macromolecule #10: 60S ribosomal protein L35
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: 60S ribosomal protein L36
+Macromolecule #13: 60S ribosomal protein L27a
+Macromolecule #14: 60S ribosomal protein L37
+Macromolecule #15: 60S ribosomal protein L39
+Macromolecule #16: 60S ribosomal protein L13
+Macromolecule #17: 60S ribosomal protein L14
+Macromolecule #18: 60S ribosomal protein L15
+Macromolecule #19: 60S ribosomal protein L13a
+Macromolecule #20: 60S ribosomal protein L37a
+Macromolecule #21: 60S ribosomal protein L18
+Macromolecule #22: 60S ribosomal protein L19
+Macromolecule #23: 60S ribosomal protein L18a
+Macromolecule #24: 60S ribosomal protein L21
+Macromolecule #25: 60S ribosomal protein L23
+Macromolecule #26: 60S ribosomal protein L26
+Macromolecule #27: 60S ribosomal protein L27
+Macromolecule #28: 60S ribosomal protein L28
+Macromolecule #29: 60S ribosomal protein L8
+Macromolecule #30: 60S ribosomal protein L35a
+Macromolecule #31: 60S ribosomal protein L6
+Macromolecule #32: 60S ribosomal protein L7
+Macromolecule #33: Protein LLP homolog
+Macromolecule #34: 60S ribosomal protein L11
+Macromolecule #35: 60S ribosomal protein L5
+Macromolecule #36: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #37: Notchless protein homolog 1
+Macromolecule #38: Ribosome biogenesis regulatory protein homolog
+Macromolecule #39: Guanine nucleotide-binding protein-like 3
+Macromolecule #40: mRNA turnover protein 4 homolog
+Macromolecule #41: G Protein Nucleolar 2
+Macromolecule #42: Coiled-coil domain-containing protein 86
+Macromolecule #45: 60S ribosomal protein L23a
+Macromolecule #46: 60S ribosomal protein L22
+Macromolecule #47: 60S ribosomal protein L31
+Macromolecule #48: 60S ribosomal protein L32
+Macromolecule #49: 60S ribosomal protein L17
+Macromolecule #50: 60S ribosomal protein L38
+Macromolecule #52: Ribosome production factor 2 homolog
+Macromolecule #53: pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
+Macromolecule #43: 28S rRNA
+Macromolecule #44: 5.8S rRMA
+Macromolecule #51: 5S RNA
+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
