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Yorodumi- EMDB-10179: mt-SSU late assembly intermediate of wild-type Trypanosoma brucei... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10179 | |||||||||
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Title | mt-SSU late assembly intermediate of wild-type Trypanosoma brucei brucei | |||||||||
Map data | mt-SSU late assembly intermediate of wild-type Trypanosoma brucei brucei | |||||||||
Sample |
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Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
Authors | Saurer M / Ramrath D / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK ...Saurer M / Ramrath D / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK / Leibundgut M / Schneider A / Boehringer D / Ban N | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Science / Year: 2019 Title: Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut ...Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban / Abstract: Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome ...Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria. | |||||||||
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_10179.map.gz | 10.6 MB | EMDB map data format | |
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Header (meta data) | emd-10179-v30.xml emd-10179.xml | 26.7 KB 26.7 KB | Display Display | EMDB header |
Images | emd_10179.png | 49.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10179 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10179 | 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_10179.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | mt-SSU late assembly intermediate of wild-type Trypanosoma brucei brucei | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.69531 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 : wild-type mt-SSU late assembly intermediate
Entire | Name: wild-type mt-SSU late assembly intermediate |
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Components |
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-Supramolecule #1: wild-type mt-SSU late assembly intermediate
Supramolecule | Name: wild-type mt-SSU late assembly intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#103 |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 15 mA |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Mitochondrial ribosomal small subunit middle assembly intermediate of wild-type Trypanosoma brucei brucei Lister strain 427 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 129032 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 13503 / Average exposure time: 1.5 sec. / Average electron dose: 75.0 e/Å2 Details: Images were collected in movie-mode at 40 frames per second |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1243432 |
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CTF correction | Software - Name: Gctf (ver. 1.06) / Details: On the fly in RELION |
Startup model | Type of model: OTHER Details: The startup model was obtained from 3D classification of all particles classified as mt-SSU (mt-SSU initial reference was determined ab-initio using RELION 3D initial model routine based on SGD). |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 6955 |
-Atomic model buiding 1
Details | Starting models of ribosomal proteins of the T. brucei mitochondrial ribosomal small subunit were taken from PDB 6HIW. Mitchondrial ribosomal small subunit assembly factors were built de novo. |
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Refinement | Protocol: OTHER |