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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 | |||||||||
![]() | human nuclear pre-60S ribosomal particle - State D - post processed | |||||||||
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![]() | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
Function / homology | ![]() 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 / : / hematopoietic stem cell homeostasis / inner cell mass cell differentiation / dendrite extension / preribosome binding / regulation of Notch signaling pathway / lamin filament ...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 / : / hematopoietic stem cell homeostasis / inner cell mass cell differentiation / dendrite extension / preribosome binding / regulation of Notch signaling pathway / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / stem cell division / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / ribosomal protein import into nucleus / 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 / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / A band / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of cyclin-dependent protein serine/threonine kinase activity / skeletal system morphogenesis / middle ear morphogenesis / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / translation at presynapse / negative regulation of cell-cell adhesion / positive regulation of dendritic spine development / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / stem cell population maintenance / homeostatic process / response to aldosterone / negative regulation of DNA replication / macrophage chemotaxis / positive regulation of telomere maintenance / lung morphogenesis / ribosomal large subunit binding / Protein hydroxylation / preribosome, large subunit precursor / Peptide chain elongation / nuclear-transcribed mRNA catabolic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / negative regulation of mitotic cell cycle / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / blastocyst development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit export from nucleus / 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 / somitogenesis / Major pathway of rRNA processing in the nucleolus and cytosol / ribosomal subunit export from nucleus / protein targeting / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / MDM2/MDM4 family protein binding / cytosolic ribosome / translation initiation factor activity / negative regulation of protein ubiquitination / embryo implantation / cellular response to interleukin-4 / ossification / innate immune response in mucosa / assembly of large subunit precursor of preribosome / DNA damage response, signal transduction by p53 class mediator / negative regulation of cell migration / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / regulation of signal transduction by p53 class mediator / positive regulation of translation / kidney development / mRNA 3'-UTR binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Zhang Y / Gao N | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 9.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 73.5 KB 73.5 KB | Display Display | ![]() |
Images | ![]() | 161.5 KB | ||
Filedesc metadata | ![]() | 17.4 KB | ||
Others | ![]() ![]() | 194.1 MB 194.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 852.7 KB | Display | ![]() |
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Full document | ![]() | 852.3 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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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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![]() | 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: ![]() |
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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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24229 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |