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Open data
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Basic information
Entry | Database: PDB / ID: 8idt | ||||||
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Title | human nuclear pre-60S ribosomal particle - State G | ||||||
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![]() | RIBOSOME / GNL2 / nuclear / pre-60S | ||||||
Function / homology | ![]() negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / negative regulation of G2/M transition of mitotic cell cycle / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / negative regulation of G2/M transition of mitotic cell cycle / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / eukaryotic 80S initiation complex / negative regulation of protein neddylation / 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 / ribosomal protein import into nucleus / 90S preribosome assembly / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / middle ear morphogenesis / negative regulation of cell-cell adhesion / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / homeostatic process / negative regulation of DNA replication / positive regulation of dendritic spine development / macrophage chemotaxis / lung morphogenesis / positive regulation of natural killer cell proliferation / ribosomal large subunit binding / Protein hydroxylation / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / blastocyst development / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of signal transduction by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / 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 / positive regulation of protein binding / 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 / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / translation initiation factor activity / embryo implantation / cytosolic ribosome / cellular response to interleukin-4 / ossification / negative regulation of cell migration / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / ribosomal large subunit biogenesis / regulation of signal transduction by p53 class mediator / innate immune response in mucosa / cytosolic ribosome assembly / mRNA 3'-UTR binding / skeletal system development / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / cellular response to gamma radiation / Regulation of expression of SLITs and ROBOs / response to insulin / bone development / mRNA 5'-UTR binding / cellular response to type II interferon / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / osteoblast differentiation / cellular response to UV / antibacterial humoral response Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 277.2 KB | Display | |
Data in CIF | ![]() | 453.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35370MC ![]() 8idyC ![]() 8ie3C ![]() 8ineC ![]() 8infC ![]() 8inkC ![]() 8ipdC ![]() 8ipxC ![]() 8ipyC ![]() 8ir1C ![]() 8ir3C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-RNA chain , 3 types, 3 molecules 582
#1: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#4: RNA chain | Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: RNA chain | Mass: 1636695.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 9 types, 9 molecules 679ARJT4z
#2: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 15230.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 83796.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 23912.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 10605.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#46: Protein | Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+60S ribosomal protein ... , 39 types, 39 molecules BCDEFGHIKLMNOPQSUVWXZabceghilm...
-Non-polymers , 4 types, 5 molecules 






#52: Chemical | ChemComp-GDP / | ||||
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#53: Chemical | #54: Chemical | ChemComp-K / | #55: Chemical | ChemComp-GTP / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: cryo-EM structure of human nuclear pre-60S ribosomal particle - State G Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 1.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175116 / Symmetry type: POINT | ||||||||||||||||||||||||
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