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Open data
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Basic information
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| Title | human nuclear pre-60S ribosomal particle - State C' | |||||||||
Map data | human nuclear pre-60S ribosomal particle - State C' - post processed | |||||||||
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Keywords | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
| Function / homology | Function and homology informationmitotic nuclear division / 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 / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / : / dendrite extension / inner cell mass cell differentiation / preribosome binding ...mitotic nuclear division / 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 / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / : / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of cellular senescence / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation / regulation of fatty acid biosynthetic process / miRNA-mediated post-transcriptional gene silencing / PeBoW complex / 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 / positive regulation of protein K63-linked deubiquitination / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / blastocyst formation / negative regulation of mitotic cell cycle / protein localization to nucleolus / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / ribosomal protein import into nucleus / regulation of G1 to G0 transition / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / alpha-beta T cell differentiation / regulation of glycolytic process / skeletal system morphogenesis / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / regulation of reactive oxygen species metabolic process / negative regulation of cell-cell adhesion / TORC2 complex binding / regulation of aerobic respiration / maturation of 5.8S rRNA / stem cell division / G1 to G0 transition / middle ear morphogenesis / stem cell population maintenance / cytoplasmic side of rough endoplasmic reticulum membrane / rRNA metabolic process / regulation of protein phosphorylation / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / positive regulation of dendritic spine development / homeostatic process / ribosomal large subunit binding / preribosome, large subunit precursor / macrophage chemotaxis / negative regulation of signal transduction by p53 class mediator / lung morphogenesis / positive regulation of telomere maintenance / positive regulation of natural killer cell proliferation / rRNA transcription / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / nuclear-transcribed mRNA catabolic process / Formation of a pool of free 40S subunits / blastocyst development / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / ubiquitin ligase inhibitor activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / ribonucleoprotein complex binding / GTP hydrolysis and joining of the 60S ribosomal subunit / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / somitogenesis / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of protein-containing complex assembly / protein targeting / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / maturation of LSU-rRNA / Notch signaling pathway / rough endoplasmic reticulum / translation initiation factor activity / MDM2/MDM4 family protein binding / embryo implantation / negative regulation of protein ubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cytosolic ribosome / cellular response to interleukin-4 Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.3 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_35649.map.gz | 11.7 MB | EMDB map data format | |
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| Header (meta data) | emd-35649-v30.xml emd-35649.xml | 83 KB 83 KB | Display Display | EMDB header |
| Images | emd_35649.png | 187.6 KB | ||
| Filedesc metadata | emd-35649.cif.gz | 19.6 KB | ||
| Others | emd_35649_half_map_1.map.gz emd_35649_half_map_2.map.gz | 194 MB 193.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35649 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8ipxMC ![]() 8idtC ![]() 8idyC ![]() 8ie3C ![]() 8ineC ![]() 8infC ![]() 8inkC ![]() 8ipdC ![]() 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_35649.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 C' - 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 C' - half2
| File | emd_35649_half_map_1.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - State C' - half2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: human nuclear pre-60S ribosomal particle - State C' - half1
| File | emd_35649_half_map_2.map | ||||||||||||
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| Annotation | human nuclear pre-60S ribosomal particle - State C' - half1 | ||||||||||||
| 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: 28S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #48: ITS2
+Macromolecule #55: 5S RNA
+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 L7a
+Macromolecule #11: 60S ribosomal protein L35
+Macromolecule #12: 60S ribosomal protein L9
+Macromolecule #13: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #14: 60S ribosomal protein L27a
+Macromolecule #15: 60S ribosomal protein L37
+Macromolecule #16: 60S ribosomal protein L39
+Macromolecule #17: 60S ribosomal protein L13
+Macromolecule #18: 60S ribosomal protein L14
+Macromolecule #19: 60S ribosomal protein L15
+Macromolecule #20: 60S ribosomal protein L13a
+Macromolecule #21: 60S ribosomal protein L37a
+Macromolecule #22: 60S ribosomal protein L18
+Macromolecule #23: 60S ribosomal protein L19
+Macromolecule #24: 60S ribosomal protein L18a
+Macromolecule #25: 60S ribosomal protein L23
+Macromolecule #26: 60S ribosomal protein L26
+Macromolecule #27: 60S ribosomal protein L28
+Macromolecule #28: 60S ribosomal protein L8
+Macromolecule #29: 60S ribosomal protein L35a
+Macromolecule #30: 60S ribosomal protein L6
+Macromolecule #31: 60S ribosomal protein L7
+Macromolecule #32: Coiled-coil domain-containing protein 86
+Macromolecule #33: Guanine nucleotide-binding protein-like 3
+Macromolecule #34: mRNA turnover protein 4 homolog
+Macromolecule #35: G Protein Nucleolar 2
+Macromolecule #36: 60S ribosomal protein L12
+Macromolecule #37: Protein LLP homolog
+Macromolecule #38: 60S ribosomal protein L11
+Macromolecule #39: 60S ribosomal protein L5
+Macromolecule #40: Notchless protein homolog 1
+Macromolecule #41: 60S ribosomal protein L21
+Macromolecule #42: GTP-binding protein 4
+Macromolecule #43: 60S ribosomal protein L17
+Macromolecule #44: 60S ribosomal protein L32
+Macromolecule #45: 60S ribosomal protein L31
+Macromolecule #46: 60S ribosomal protein L22
+Macromolecule #47: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #49: Ribosomal L1 domain-containing protein 1
+Macromolecule #50: 60S ribosomal protein L7-like 1
+Macromolecule #51: 60S ribosomal protein L36
+Macromolecule #52: 60S ribosomal protein L34
+Macromolecule #53: 60S ribosomal protein L27
+Macromolecule #54: 60S ribosomal protein L38
+Macromolecule #56: Pescadillo homolog
+Macromolecule #57: 60S ribosomal protein L23a
+Macromolecule #58: Ribosome biogenesis protein NOP53
+Macromolecule #59: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #60: 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
