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Yorodumi- EMDB-2490: Structure of the 39S Large Subunit of the Mammalian Mitochondrial... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2490 | |||||||||
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Title | Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome | |||||||||
Map data | Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome | |||||||||
Sample |
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Keywords | mammalian mitochondrial ribosome / 39S large ribosomal subunit / translation / ribosomal proteins / rRNA / polypeptide exit site / membrane association | |||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / mitochondrial translation / organelle membrane / RNA processing / large ribosomal subunit / double-stranded RNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Sus scrofa domesticus (domestic pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Greber BJ / Boehringer D / Leitner A / Bieri P / Voigts-Hoffmann F / Erzberger JP / Leibundgut M / Aebersold R / Ban N | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Architecture of the large subunit of the mammalian mitochondrial ribosome. Authors: Basil J Greber / Daniel Boehringer / Alexander Leitner / Philipp Bieri / Felix Voigts-Hoffmann / Jan P Erzberger / Marc Leibundgut / Ruedi Aebersold / Nenad Ban / Abstract: Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by ...Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain. | |||||||||
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_2490.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-2490-v30.xml emd-2490.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
Images | EMD-2490-image_EMDB_ray_500px.png | 129.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2490 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2490 | HTTPS FTP |
-Validation report
Summary document | emd_2490_validation.pdf.gz | 331 KB | Display | EMDB validaton report |
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Full document | emd_2490_full_validation.pdf.gz | 330.1 KB | Display | |
Data in XML | emd_2490_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2490 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2490 | HTTPS FTP |
-Related structure data
Related structure data | 4ce4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_2490.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.41 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 : 39S large subunit of the porcine mitochondrial ribosome
Entire | Name: 39S large subunit of the porcine mitochondrial ribosome |
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Components |
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-Supramolecule #1000: 39S large subunit of the porcine mitochondrial ribosome
Supramolecule | Name: 39S large subunit of the porcine mitochondrial ribosome type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 1.6 MDa |
-Supramolecule #1: 39S large subunit of the mitochondrial ribosome
Supramolecule | Name: 39S large subunit of the mitochondrial ribosome / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Ref GO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kGO3A00057 61ampajax1 classpoptr giGO000576 1ispandiv |
Source (natural) | Organism: Sus scrofa domesticus (domestic pig) / synonym: domestic pig / Tissue: Liver / Organelle: Mitochondrion |
Molecular weight | Theoretical: 1.6 MDa |