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- EMDB-16562: Structure of the yeast delta uL16m mitochondrial ribosome assembl... -
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Open data
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Basic information
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Title | Structure of the yeast delta uL16m mitochondrial ribosome assembly intermediate - State 1 | |||||||||||||||
![]() | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, consensus map | |||||||||||||||
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![]() | Yeast mitochondrial ribosome / delta uL16 / RIBOSOME | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
![]() | Conrad J / Rathore S / Barrientos A | |||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: The late stages of yeast mitoribosome large subunit biogenesis Authors: Rathore S / Conrad J / De Silva D / Ferrari A / Bouquio D / Kim H-J / Urlaub H / Ott M / Barrientos A | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 161.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.3 KB 20.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 130.2 KB | ||
Filedesc metadata | ![]() | 4.5 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 163.6 MB 160 MB 161.1 MB 140.6 MB 140.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 970.3 KB | Display | ![]() |
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Full document | ![]() | 969.8 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, consensus map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large...
File | emd_16562_additional_1.map | ||||||||||||
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Annotation | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, LSU body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, CP
File | emd_16562_additional_2.map | ||||||||||||
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Annotation | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, CP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large...
File | emd_16562_additional_3.map | ||||||||||||
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Annotation | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, E-site tRNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State 1, delta uL16m, yeast mitochondrial ribosome, large...
File | emd_16562_half_map_1.map | ||||||||||||
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Annotation | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State 1, delta uL16m, yeast mitochondrial ribosome, large...
File | emd_16562_half_map_2.map | ||||||||||||
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Annotation | State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Large subunit of the yeast mitochondrial ribosome- State 1, delta...
Entire | Name: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m |
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Components |
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-Supramolecule #1: Large subunit of the yeast mitochondrial ribosome- State 1, delta...
Supramolecule | Name: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m type: complex / ID: 1 / Parent: 0 Details: Mitoribosomal particles from an uL16m-deletion strain were purified by sucrose cushion sedimentation of mitochondrial extracts prepared in the presence of 20% Mg2+ and 1% Triton X-100. This ...Details: Mitoribosomal particles from an uL16m-deletion strain were purified by sucrose cushion sedimentation of mitochondrial extracts prepared in the presence of 20% Mg2+ and 1% Triton X-100. This approach revealed the structures of novel mitoribosome assembly intermediates. After processing, the structural characterization of the uL16m-deletion mitoribosome particles allowed us to define two major states: state 1, state 2. |
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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
Buffer | pH: 7.4 |
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Grid | Model: EMS Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |