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Open data
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Basic information
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Title | Enp1TAP-S21_A, consensus Refinement | |||||||||
![]() | Enp1TAP-S21_A, consensus Refinement | |||||||||
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![]() | ribosomal assembly state / ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Milkereit P / Poell G | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors. Authors: Gisela Pöll / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit / ![]() Abstract: RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work ...RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required for the stabilisation and maturation of SSU precursors at specific post-nucleolar stages. Here, we analysed the role of S0-cluster formation for rRNA folding. Structures of SSU precursors isolated from yeast S0-cluster expression mutants or control strains were analysed by cryogenic electron microscopy. The obtained resolution was sufficient to detect individual 2'-O-methyl RNA modifications using an unbiased scoring approach. The data show how S0-cluster formation enables the initial recruitment of the pre-rRNA processing factor Nob1 in yeast. Furthermore, they reveal hierarchical effects on the pre-rRNA folding pathway, including the final maturation of the central pseudoknot. Based on these structural insights we discuss how formation of the S0-cluster determines at this early cytoplasmic assembly checkpoint if SSU precursors further mature or are degraded. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 193.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
Images | ![]() | 175.2 KB | ||
Filedesc metadata | ![]() | 4.4 KB | ||
Others | ![]() ![]() | 194.4 MB 194.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Enp1TAP-S21_A, consensus Refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.968 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Enp1TAP-S21 A, consensus Refinement, halfmap 1
File | emd_16346_half_map_1.map | ||||||||||||
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Annotation | Enp1TAP-S21_A, consensus Refinement, halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Enp1TAP-S21 A, consensus Refinement, halfmap 2
File | emd_16346_half_map_2.map | ||||||||||||
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Annotation | Enp1TAP-S21_A, consensus Refinement, halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Enp1-TAP associated immature ribosomal particles from S. cerevisi...
Entire | Name: Enp1-TAP associated immature ribosomal particles from S. cerevisiae depleted of rpS21/eS21 |
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Components |
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-Supramolecule #1: Enp1-TAP associated immature ribosomal particles from S. cerevisi...
Supramolecule | Name: Enp1-TAP associated immature ribosomal particles from S. cerevisiae depleted of rpS21/eS21 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 200 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8302 / Average exposure time: 4.8 sec. / Average electron dose: 40.0 e/Å2 |
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Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) |
Final 3D classification | Software - Name: RELION (ver. 4.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 132563 |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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