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Yorodumi- EMDB-3556: Yeast mitochondrial ribosome - large subunit (fitted to EMD 3551) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3556 | |||||||||
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Title | Yeast mitochondrial ribosome - large subunit (fitted to EMD 3551) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Desai N / Brown A / Amunts A / Ramakrishnan V | |||||||||
Citation | Journal: Science / Year: 2017 Title: The structure of the yeast mitochondrial ribosome. Authors: Nirupa Desai / Alan Brown / Alexey Amunts / V Ramakrishnan / Abstract: Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the ...Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation. | |||||||||
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_3556.map.gz | 9.5 MB | EMDB map data format | |
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Header (meta data) | emd-3556-v30.xml emd-3556.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_3556.png | 138.6 KB | ||
Others | emd_3556_half_map_1.map.gz emd_3556_half_map_2.map.gz | 120.8 MB 120.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3556 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3556 | HTTPS FTP |
-Validation report
Summary document | emd_3556_validation.pdf.gz | 371 KB | Display | EMDB validaton report |
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Full document | emd_3556_full_validation.pdf.gz | 370.1 KB | Display | |
Data in XML | emd_3556_validation.xml.gz | 12.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3556 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3556 | HTTPS FTP |
-Related structure data
Related structure data | 3551C 3552C 3553C 3554C 3555C 5mrcC 5mreC 5mrfC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10107 (Title: The Structure of the Yeast Mitochondrial Ribosome / Data size: 138.6 Data #1: Yeast mitochondrial ribosome - shiny particles [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3556.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_3556_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3556_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Yeast mitochondrial ribosome - large subunit
Entire | Name: Yeast mitochondrial ribosome - large subunit |
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Components |
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-Supramolecule #1: Yeast mitochondrial ribosome - large subunit
Supramolecule | Name: Yeast mitochondrial ribosome - large subunit / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 23.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: RELION (ver. 1.4) |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 221875 |
Initial angle assignment | Type: OTHER / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4) |