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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3199 | |||||||||
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Title | Cryo-EM structure of the Rix1-Rea1 pre-60S particle | |||||||||
![]() | Cryo-EM structure of the Rix1-Rea1 pre-60S particle | |||||||||
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![]() | ribosome / ribosome biogenesis / ribosome assembly / pre-60S / 5S RNP / assembly intermediate / cryo-EM / Rea1 / Rix1 complex / Sda1 | |||||||||
Function / homology | ![]() 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 / nuclear-transcribed mRNA catabolic process / 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 ...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 / nuclear-transcribed mRNA catabolic process / 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 / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / 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 from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / ribosomal large subunit assembly / 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 / cell cycle / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.5 Å | |||||||||
![]() | Barrio-Garcia C / Thoms M / Flemming D / Kater L / Berninghausen O / Bassler J / Beckmann R / Hurt E | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 18.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() | 918.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 215.7 KB | Display | ![]() |
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Full document | ![]() | 214.8 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jcsMC ![]() 3200C ![]() 3203C ![]() 3207C ![]() 5fl8 M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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 | Cryo-EM structure of the Rix1-Rea1 pre-60S particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.069 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Rix1-Rea1 pre60S particle
Entire | Name: Rix1-Rea1 pre60S particle |
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Components |
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-Supramolecule #1000: Rix1-Rea1 pre60S particle
Supramolecule | Name: Rix1-Rea1 pre60S particle / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: pre-60S particle
Supramolecule | Name: pre-60S particle / type: complex / ID: 1 / Name.synonym: pre-60S / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: LSU 60S |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.06 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris-HCl, 100 mM NaCl, 1.5 mM or 5 mM MgCl2 |
Grid | Details: The freshly prepared pre-60S sample was applied to 2 nm pre-coated Quantifoil holey carbon supported grids and vitrified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jun 12, 2014 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 2659 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | The particles were selected using the automatic selection program SIGNATURE |
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CTF correction | Details: Subvolumes |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: OTHER / Software - Name: Signature, Spider / Number images used: 15749 |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 3j64 |
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Software | Name: Chimera, MDFF, Coot |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-5jcs: |
-Atomic model buiding 2
Initial model | PDB ID: ![]() 3u5d |
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Software | Name: Chimera, MDFF, Coot |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-5jcs: |
-Atomic model buiding 3
Initial model | PDB ID: ![]() 3u5e |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5jcs: |
-Atomic model buiding 4
Initial model | PDB ID: ![]() 3j65 |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5jcs: |