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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' | |||||||||
![]() | human nuclear pre-60S ribosomal particle - State C' - post processed | |||||||||
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![]() | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
Function / homology | ![]() 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 / inner cell mass cell differentiation / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension ...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 / inner cell mass cell differentiation / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / regulation of cellular senescence / regulation of Notch signaling pathway / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / positive regulation of protein sumoylation / PeBoW complex / negative regulation of signal transduction by p53 class mediator / miRNA-mediated gene silencing by inhibition of translation / 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 / stem cell division / 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 / : / blastocyst formation / positive regulation of protein K63-linked deubiquitination / protein localization to nucleolus / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TORC2 complex binding / GAIT complex / A band / G1 to G0 transition / middle ear morphogenesis / regulation of reactive oxygen species metabolic process / alpha-beta T cell differentiation / skeletal system morphogenesis / translation at presynapse / regulation of glycolytic process / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of dendritic spine development / negative regulation of cell-cell adhesion / negative regulation of ubiquitin protein ligase activity / regulation of aerobic respiration / maturation of 5.8S rRNA / regulation of cyclin-dependent protein serine/threonine kinase activity / stem cell population maintenance / response to aldosterone / homeostatic process / negative regulation of DNA replication / rRNA metabolic process / macrophage chemotaxis / lung morphogenesis / mitotic G2 DNA damage checkpoint signaling / positive regulation of telomere maintenance / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / rRNA transcription / preribosome, large subunit precursor / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / nuclear-transcribed mRNA catabolic process / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / negative regulation of mitotic cell cycle / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of protein-containing complex assembly / protein targeting / regulation of protein phosphorylation / protein-RNA complex assembly / somitogenesis / ribosomal subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / ribonucleoprotein complex binding / : / rough endoplasmic reticulum / Notch signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / MDM2/MDM4 family protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 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 | ![]() | 11.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 80.3 KB 80.3 KB | Display Display | ![]() |
Images | ![]() | 187.6 KB | ||
Filedesc metadata | ![]() | 19 KB | ||
Others | ![]() ![]() | 194 MB 193.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 944.7 KB | Display | ![]() |
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Full document | ![]() | 944.3 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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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![]() | 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4919 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |