+Open data
-Basic information
Entry | Database: PDB / ID: 5jcs | |||||||||
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Title | CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE | |||||||||
Components |
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Keywords | RIBOSOME / pre-60S ribosome rix1 rea1 | |||||||||
Function / homology | Function and homology information protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Hydrolases / traversing start control point of mitotic cell cycle / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Hydrolases / traversing start control point of mitotic cell cycle / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / regulation of translational fidelity / ribosomal subunit export from nucleus / 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 / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / proteolysis / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | |||||||||
Authors | Barrio-Garcia, C. / Thoms, M. / Flemming, D. / Kater, L. / Berninghausen, O. / Bassler, J. / Beckmann, R. / Hurt, E. | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling. Authors: Clara Barrio-Garcia / Matthias Thoms / Dirk Flemming / Lukas Kater / Otto Berninghausen / Jochen Baßler / Roland Beckmann / Ed Hurt / Abstract: Ribosome synthesis is catalyzed by ∼200 assembly factors, which facilitate efficient production of mature ribosomes. Here, we determined the cryo-EM structure of a Saccharomyces cerevisiae ...Ribosome synthesis is catalyzed by ∼200 assembly factors, which facilitate efficient production of mature ribosomes. Here, we determined the cryo-EM structure of a Saccharomyces cerevisiae nucleoplasmic pre-60S particle containing the dynein-related 550-kDa Rea1 AAA(+) ATPase and the Rix1 subcomplex. This particle differs from its preceding state, the early Arx1 particle, by two massive structural rearrangements: an ∼180° rotation of the 5S ribonucleoprotein complex and the central protuberance (CP) rRNA helices, and the removal of the 'foot' structure from the 3' end of the 5.8S rRNA. Progression from the Arx1 to the Rix1 particle was blocked by mutational perturbation of the Rix1-Rea1 interaction but not by a dominant-lethal Rea1 AAA(+) ATPase-ring mutant. After remodeling, the Rix1 subcomplex and Rea1 become suitably positioned to sense correct structural maturation of the CP, which allows unidirectional progression toward mature ribosomes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5jcs.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5jcs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5jcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jcs_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5jcs_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5jcs_validation.xml.gz | 242.3 KB | Display | |
Data in CIF | 5jcs_validation.cif.gz | 421.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/5jcs ftp://data.pdbj.org/pub/pdb/validation_reports/jc/5jcs | HTTPS FTP |
-Related structure data
Related structure data | 3199MC 3200C 3203C 3207C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
+60S ribosomal protein ... , 37 types, 37 molecules AcBdCeDfEgFhGiHjIkJlKLMNpOPQRS...
-Protein , 6 types, 6 molecules morstu
#22: Protein | Mass: 26476.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TIF6, CDC95, YPR016C, LPZ15C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12522 |
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#26: Protein | Mass: 74531.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NOG1, YPL093W, LPG15W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02892 |
#32: Protein | Mass: 86755.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SDA1, YGR245C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53313 |
#34: Protein | Mass: 559951.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MDN1, REA1, YLR106C, L2901, L8004.13 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12019 |
#36: Protein | Mass: 24027.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RLP24, YLR009W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q07915 |
#38: Protein | Mass: 65290.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ARX1, YDR101C, YD8557.10c / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03862, Hydrolases |
-Ribosome assembly ... , 2 types, 2 molecules nq
#24: Protein | Mass: 27098.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MRT4, YKL009W, YKL160 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33201 |
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#30: Protein | Mass: 57106.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RSA4, YCR072C, YCR72C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25382 |
-RNA chain , 3 types, 3 molecules xyz
#40: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822 |
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#42: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1036126960 |
#44: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039022925 |
-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: Rix1-Rea1 pre-60S particle / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 15749 / Symmetry type: POINT |