+Open data
-Basic information
Entry | Database: PDB / ID: 8hfr | ||||||
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Title | NPC-trapped pre-60S particle | ||||||
Components |
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Keywords | RIBOSOME / pre-60S ribosome | ||||||
Function / homology | Function and homology information nuclear RNA export factor complex / regulation of ribosomal subunit export from nucleus / nuclear pore central transport channel / Hydrolases / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...nuclear RNA export factor complex / regulation of ribosomal subunit export from nucleus / nuclear pore central transport channel / Hydrolases / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / tRNA processing / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / poly(A)+ mRNA export from nucleus / response to cycloheximide / porin activity / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / U5 snRNA binding / regulation of translational fidelity / ribosomal subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / Neutrophil degranulation / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / metallopeptidase activity / protein transport / ribosome biogenesis / ATPase binding / protein-macromolecule adaptor activity / 5S rRNA binding / large ribosomal subunit rRNA binding / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / nucleolus / GTP binding / proteolysis / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å | ||||||
Authors | Li, Z.Q. / Chen, S.J. / Sui, S.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: Nuclear export of pre-60S particles through the nuclear pore complex. Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Huiqin Xu / Xiaoyun Yang / Peiyi Wang / Ning Gao / Sen-Fang Sui / Abstract: The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal ...The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hfr.cif.gz | 3.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8hfr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8hfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hfr_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8hfr_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8hfr_validation.xml.gz | 303.4 KB | Display | |
Data in CIF | 8hfr_validation.cif.gz | 529.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/8hfr ftp://data.pdbj.org/pub/pdb/validation_reports/hf/8hfr | HTTPS FTP |
-Related structure data
Related structure data | 34725MC 8hbnC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+60S ribosomal protein ... , 37 types, 37 molecules h1g2b3B4V5O6f7F8cCCDUFdGeHLLDORPMQmSYUnYSZiaIbXcjhliHjQkTlNo...
-Nucleolar GTP-binding protein ... , 2 types, 2 molecules v9rA
#9: Protein | Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NOG2, YNR053C, N3484 / Strain: ATCC 204508 / S288c / References: UniProt: P53742 |
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#10: Protein | Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NOG1, YPL093W, LPG15W / Strain: ATCC 204508 / S288c / References: UniProt: Q02892 |
-Ribosome biogenesis protein ... , 3 types, 3 molecules tBqJxd
#11: Protein | Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RLP24, YLR009W / Strain: ATCC 204508 / S288c / References: UniProt: Q07915 |
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#19: Protein | Mass: 19322.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: ALB1, YJL122W, J0723 / Strain: ATCC 204508 / S288c / References: UniProt: P47019 |
#36: Protein | Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NSA2, YER126C, SYGP-ORF47 / Strain: ATCC 204508 / S288c / References: UniProt: P40078 |
-Protein , 10 types, 14 molecules yExIDKFRBtANCWEXpTvVWgsmzpox
#14: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: TIF6, CDC95, YPR016C, LPZ15C / Strain: ATCC 204508 / S288c / References: UniProt: Q12522 | ||||||||||||||
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#18: Protein | Mass: 23934.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: ECM1, SIM1, YAL059W / Strain: ATCC 204508 / S288c / References: UniProt: P39715 | ||||||||||||||
#20: Protein | Mass: 20802.506 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: MTR2, YKL186C / Strain: ATCC 204508 / S288c / References: UniProt: P34232 #23: Protein | Mass: 67417.477 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: MEX67, YPL169C, P2520 / Strain: ATCC 204508 / S288c / References: UniProt: Q99257 #28: Protein | | Mass: 65290.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: ARX1, YDR101C, YD8557.10c / References: UniProt: Q03862, Hydrolases #30: Protein | | Mass: 59167.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NMD3, YHR170W / Strain: ATCC 204508 / S288c / References: UniProt: P38861 #39: Protein | | Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: MRT4, YKL009W, YKL160 / Strain: ATCC 204508 / S288c / References: UniProt: P33201 #45: Protein | | Mass: 20883.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: TMA16, YOR252W / Strain: ATCC 204508 / S288c / References: UniProt: Q08687 #48: Protein | | Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: YBL028C, YBL0423 / Strain: ATCC 204508 / S288c / References: UniProt: P38202 #55: Protein | | Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: BUD20, YLR074C / Strain: ATCC 204508 / S288c / References: UniProt: Q08004 |
-YEAST 60S ribosomal protein ... , 2 types, 2 molecules KMAs
#22: Protein | Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL12A / References: UniProt: P0CX53 |
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#51: Protein | Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL1A,SSM1,SSM1A / Strain: ATCC 204508 / S288c / References: UniProt: P0CX43 |
-RNA chain , 3 types, 3 molecules 1e2f3n
#37: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: NR_132207 |
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#38: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1039023795 |
#46: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1669301378 |
-Non-polymers , 1 types, 237 molecules
#58: Chemical | ChemComp-MG / |
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-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 |
-Sample preparation
Component | Name: NPC-trapped pre-60S ribosome / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86343 / Symmetry type: POINT |