+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2914 | |||||||||
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Title | Cryo-EM reconstruction of the mammalian 55S mitoribosome | |||||||||
Map data | Reconstruction of the 55S mammalian mitoribosome | |||||||||
Sample |
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Keywords | mammalian mitochondrial ribosome / 55S mitoribosome / translation / ribosomal proteins / rRNA / tRNA / mRNA / decoding / exit tunnel | |||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial ribosome assembly / mitochondrial translational elongation / microprocessor complex / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase ...Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial ribosome assembly / mitochondrial translational elongation / microprocessor complex / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding / organelle membrane / RNA processing / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / 5S rRNA binding / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Greber BJ / Bieri P / Leibundgut M / Leitner A / Aebersold R / Boehringer D / Ban N | |||||||||
Citation | Journal: Science / Year: 2015 Title: Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome. Authors: Basil J Greber / Philipp Bieri / Marc Leibundgut / Alexander Leitner / Ruedi Aebersold / Daniel Boehringer / Nenad Ban / Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of ...Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity. | |||||||||
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_2914.map.gz | 14.2 MB | EMDB map data format | |
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Header (meta data) | emd-2914-v30.xml emd-2914.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | EMDB_2914_55S_500px.png | 360.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2914 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2914 | HTTPS FTP |
-Related structure data
Related structure data | 5aj4MC 2913C 5aj3C 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_2914.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the 55S mammalian mitoribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 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 : 55S mammalian mitochondrial ribosome
Entire | Name: 55S mammalian mitochondrial ribosome |
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Components |
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-Supramolecule #1000: 55S mammalian mitochondrial ribosome
Supramolecule | Name: 55S mammalian mitochondrial ribosome / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 2 |
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Molecular weight | Theoretical: 2.7 MDa |
-Supramolecule #1: 28S small subunit of the mitochondrial ribosome
Supramolecule | Name: 28S small subunit of the mitochondrial ribosome / type: complex / ID: 1 / Recombinant expression: No Ribosome-details: ribosome-eukaryote: SSU mitochondrial 28S, SSU mitochondrial RNA 12S |
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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 (pig) / synonym: Domestic pig / Tissue: Liver / Organelle: Mitochondrion |
Molecular weight | Theoretical: 1.1 MDa |
-Supramolecule #2: 39S large subunit of the mitochondrial ribosome
Supramolecule | Name: 39S large subunit of the mitochondrial ribosome / type: complex / ID: 2 / Recombinant expression: No Ribosome-details: ribosome-eukaryote: LSU mitochondrial 39S, LSU mitochondrial RNA 16S |
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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 (pig) / synonym: Domestic pig / Tissue: Liver / Organelle: mitochondrion |
Molecular weight | Theoretical: 1.6 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 20 mM HEPES-KOH, 50 mM KCl, 1 mM DTT, 40 mM MgCl2 |
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Grid | Details: 200 mesh Quantifoil R 2/2 holey carbon grids with a thin continuous carbon support film applied |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy #1
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100720 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Microscopy ID | 1 |
Details | movie mode readout in FEI EPU: 7 frames per exposure |
Date | May 3, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2 Details: movie mode readout in FEI EPU: 7 frames per exposure |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #2
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100720 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Microscopy ID | 2 |
Details | movie mode readout in FEI EPU: 7 frames per exposure |
Date | May 30, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2 Details: movie mode readout in FEI EPU: 7 frames per exposure |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: per detector frame |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, 1.2, 1.3 / Number images used: 60872 |
Details | Particles were selected in batchboxer (EMAN 1.9) and extracted using RELION 1.2. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The coordinate model of the 39S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and O (proteins). |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-5aj4: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The coordinate model of the 39S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and O (proteins). |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-5aj4: |