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Yorodumi- EMDB-3203: Cryo-EM structure of the Rix1-Rea1 K1089A mutant pre-60S particle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3203 | |||||||||
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Title | Cryo-EM structure of the Rix1-Rea1 K1089A mutant pre-60S particle | |||||||||
Map data | Reconstruction of Rix1-Rea1 K1089A mutant particle | |||||||||
Sample |
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Keywords | ribosome / ribosome biogenesis / ribosome assembly / pre-60S / 5S RNP / assembly intermediate / cryo-EM / Rea1 / Rix1 complex / Sda1 | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3203.map.gz | 38.2 MB | EMDB map data format | |
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Header (meta data) | emd-3203-v30.xml emd-3203.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | EMD-3203_Rix1-Rea1-A3.png | 2.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3203 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3203 | HTTPS FTP |
-Validation report
Summary document | emd_3203_validation.pdf.gz | 211.6 KB | Display | EMDB validaton report |
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Full document | emd_3203_full_validation.pdf.gz | 210.8 KB | Display | |
Data in XML | emd_3203_validation.xml.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3203 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3203 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3203.map.gz / Format: CCP4 / Size: 443.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Rix1-Rea1 K1089A mutant particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.376 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rix1-Rea1 K1089A mutant pre60S particle
Entire | Name: Rix1-Rea1 K1089A mutant pre60S particle |
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Components |
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-Supramolecule #1000: Rix1-Rea1 K1089A mutant pre60S particle
Supramolecule | Name: Rix1-Rea1 K1089A mutant 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: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.548 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jul 31, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1672 / Average electron dose: 36 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.58 µm / Nominal defocus min: 1.26 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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: 8.9 Å / Resolution method: OTHER / Software - Name: Signature, Spider / Number images used: 16341 |