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Open data
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Basic information
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Title | human nuclear pre-60S ribosomal particle - State B' | |||||||||
![]() | state-B | |||||||||
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![]() | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
Function / homology | ![]() protein localization to nucleoplasm / inner cell mass cell differentiation / 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 / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension ...protein localization to nucleoplasm / inner cell mass cell differentiation / 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 / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / negative regulation of signal transduction by p53 class mediator / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / positive regulation of telomere maintenance / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / positive regulation of protein K63-linked deubiquitination / blastocyst formation / protein localization to nucleolus / TORC2 complex binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GAIT complex / middle ear morphogenesis / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / mitotic metaphase chromosome alignment / regulation of aerobic respiration / response to aldosterone / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / rRNA metabolic process / G1 to G0 transition / negative regulation of cell-cell adhesion / homeostatic process / positive regulation of dendritic spine development / maturation of 5.8S rRNA / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / ribosomal large subunit binding / mitotic G2 DNA damage checkpoint signaling / Peptide chain elongation / Selenocysteine synthesis / rRNA transcription / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / nuclear-transcribed mRNA catabolic process / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / negative regulation of mitotic cell cycle / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / hematopoietic progenitor cell differentiation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / cellular response to actinomycin D / ribonucleoprotein complex binding / somitogenesis / cytosolic ribosome / 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 / MDM2/MDM4 family protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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 | ![]() | 13.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 80.4 KB 80.4 KB | Display Display | ![]() |
Images | ![]() | 162.2 KB | ||
Filedesc metadata | ![]() | 19 KB | ||
Others | ![]() ![]() | 194.3 MB 194.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ir3MC ![]() 8idtC ![]() 8idyC ![]() 8ie3C ![]() 8ineC ![]() 8infC ![]() 8inkC ![]() 8ipdC ![]() 8ipxC ![]() 8ipyC ![]() 8ir1C 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 | state-B | ||||||||||||||||||||
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: state-B
File | emd_35673_half_map_1.map | ||||||||||||
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Annotation | state-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: state-B
File | emd_35673_half_map_2.map | ||||||||||||
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Annotation | state-B | ||||||||||||
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: Zinc finger protein 593
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4
+Macromolecule #8: 60S ribosomal protein L30
+Macromolecule #9: 60S ribosomal protein L34
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L35
+Macromolecule #12: 60S ribosomal protein L9
+Macromolecule #13: 60S ribosomal protein L36
+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 L21
+Macromolecule #26: 60S ribosomal protein L23
+Macromolecule #27: 60S ribosomal protein L26
+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 L22
+Macromolecule #46: 60S ribosomal protein L31
+Macromolecule #47: 60S ribosomal protein L32
+Macromolecule #48: 60S ribosomal protein L17
+Macromolecule #49: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #50: Ribosomal L1 domain-containing protein 1
+Macromolecule #51: 60S ribosomal protein L27
+Macromolecule #52: Ribosome production factor 2 homolog
+Macromolecule #54: Pescadillo homolog
+Macromolecule #55: Ribosome biogenesis protein NOP53
+Macromolecule #56: 60S ribosomal protein L38
+Macromolecule #57: 60S ribosomal protein L7-like 1
+Macromolecule #58: 60S ribosomal protein L23a
+Macromolecule #43: 5.8S rRNA
+Macromolecule #44: 28S rRNA
+Macromolecule #53: 5S RNA
+Macromolecule #59: ITS2
+Macromolecule #60: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #61: 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18549 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |