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Yorodumi- EMDB-12568: 55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12568 | |||||||||
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Title | 55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E) | |||||||||
Map data | map filtered to 4.6A instead of FSC weighting in Relion | |||||||||
Sample |
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Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / ribonuclease III activity / ribosome disassembly ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / ribonuclease III activity / ribosome disassembly / microprocessor complex / Mitochondrial translation termination / ribosomal subunit / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / organelle membrane / ribosomal large subunit binding / positive regulation of proteolysis / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / double-stranded RNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / mRNA binding / nucleotide binding / synapse / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Kummer E / Schubert K / Ban N | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Authors: Eva Kummer / Katharina Noel Schubert / Tanja Schoenhut / Alain Scaiola / Nenad Ban / Abstract: The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as ...The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process. | |||||||||
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_12568.map.gz | 393.5 MB | EMDB map data format | |
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Header (meta data) | emd-12568-v30.xml emd-12568.xml | 121 KB 121 KB | Display Display | EMDB header |
Images | emd_12568.png | 63 KB | ||
Masks | emd_12568_msk_1.map | 421.9 MB | Mask map | |
Others | emd_12568_additional_1.map.gz emd_12568_additional_2.map.gz emd_12568_additional_3.map.gz emd_12568_half_map_1.map.gz emd_12568_half_map_2.map.gz | 48.4 MB 639.8 MB 337.8 MB 340 MB 340.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12568 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12568 | HTTPS FTP |
-Validation report
Summary document | emd_12568_validation.pdf.gz | 588.1 KB | Display | EMDB validaton report |
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Full document | emd_12568_full_validation.pdf.gz | 587.6 KB | Display | |
Data in XML | emd_12568_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_12568_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12568 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12568 | HTTPS FTP |
-Related structure data
Related structure data | 7nsiMC 7nqhC 7nqlC 7nshC 7nsjC 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_12568.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map filtered to 4.6A instead of FSC weighting in Relion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12568_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: masked postprocessed map (map filtered to 4.6A instead...
File | emd_12568_additional_1.map | ||||||||||||
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Annotation | masked postprocessed map (map filtered to 4.6A instead of FSC weighting in Relion) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 5x supersampled map (map filtered to 4.6A instead...
File | emd_12568_additional_2.map | ||||||||||||
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Annotation | 5x supersampled map (map filtered to 4.6A instead of FSC weighting in Relion) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: full map from 3D gold-standard refinement
File | emd_12568_additional_3.map | ||||||||||||
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Annotation | full map from 3D gold-standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12568_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12568_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)
+Supramolecule #1: 55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)
+Supramolecule #2: 55S mammalian mitochondrial ribosome
+Supramolecule #3: Ribosome-recycling factor, mitochondrial
+Macromolecule #1: 39S ribosomal protein L27, mitochondrial
+Macromolecule #2: 39S ribosomal protein L28, mitochondrial
+Macromolecule #3: Mitochondrial ribosomal protein L47
+Macromolecule #4: 39S ribosomal protein L30, mitochondrial
+Macromolecule #5: Mitochondrial ribosomal protein L55
+Macromolecule #6: bL32m
+Macromolecule #7: 39S ribosomal protein L33, mitochondrial
+Macromolecule #9: 39S ribosomal protein L34, mitochondrial
+Macromolecule #10: Ribosomal_L2_C domain-containing protein
+Macromolecule #11: ICT1
+Macromolecule #12: Mitochondrial ribosomal protein L4
+Macromolecule #13: Ribosome-recycling factor, mitochondrial
+Macromolecule #14: 39S ribosomal protein L9, mitochondrial
+Macromolecule #15: 39S ribosomal protein L10, mitochondrial isoform a
+Macromolecule #16: 39S ribosomal protein L11, mitochondrial isoform a
+Macromolecule #17: 39S ribosomal protein L13, mitochondrial
+Macromolecule #18: uL14m
+Macromolecule #19: 39S ribosomal protein L15, mitochondrial
+Macromolecule #20: 39S ribosomal protein L16, mitochondrial
+Macromolecule #21: 39S ribosomal protein L17, mitochondrial
+Macromolecule #22: 39S ribosomal protein L18, mitochondrial isoform 1
+Macromolecule #23: 39S ribosomal protein L19, mitochondrial
+Macromolecule #24: 39S ribosomal protein L20, mitochondrial isoform 1
+Macromolecule #25: 39S ribosomal protein L21, mitochondrial isoform d
+Macromolecule #26: 39S ribosomal protein L22, mitochondrial
+Macromolecule #27: 39S ribosomal protein L23, mitochondrial
+Macromolecule #28: 39S ribosomal protein L24, mitochondrial isoform X1
+Macromolecule #29: 39S ribosomal protein L37, mitochondrial
+Macromolecule #30: 39S ribosomal protein L38, mitochondrial
+Macromolecule #31: TGS domain-containing protein
+Macromolecule #32: Mitochondrial ribosomal protein L40
+Macromolecule #33: Mitochondrial ribosomal protein L41
+Macromolecule #34: mL42
+Macromolecule #35: 39S ribosomal protein L43, mitochondrial isoform X2
+Macromolecule #36: 39S ribosomal protein L35, mitochondrial
+Macromolecule #37: 39S ribosomal protein L44, mitochondrial
+Macromolecule #38: Mitochondrial ribosomal protein L45
+Macromolecule #39: 39S ribosomal protein L46, mitochondrial
+Macromolecule #40: 39S ribosomal protein L48, mitochondrial
+Macromolecule #41: 39S ribosomal protein L49, mitochondrial
+Macromolecule #42: 39S ribosomal protein L50, mitochondrial
+Macromolecule #43: 39S ribosomal protein L51, mitochondrial
+Macromolecule #44: 39S ribosomal protein L52, mitochondrial
+Macromolecule #45: mL53
+Macromolecule #46: 39S ribosomal protein L54, mitochondrial
+Macromolecule #47: Mitochondrial ribosomal protein L57
+Macromolecule #48: Mitochondrial ribosomal protein L58
+Macromolecule #49: 39S ribosomal protein L59, mitochondrial
+Macromolecule #50: 39S ribosomal protein S30, mitochondrial
+Macromolecule #51: Mitochondrial ribosomal protein S18A
+Macromolecule #53: Ribosomal protein
+Macromolecule #57: 28S ribosomal protein S2, mitochondrial
+Macromolecule #58: 28S ribosomal protein S24, mitochondrial
+Macromolecule #59: 28S ribosomal protein S5, mitochondrial isoform X2
+Macromolecule #60: Mitochondrial ribosomal protein S6
+Macromolecule #61: 28S ribosomal protein S7, mitochondrial
+Macromolecule #62: 28S ribosomal protein S9, mitochondrial
+Macromolecule #63: 28S ribosomal protein S10, mitochondrial
+Macromolecule #64: Mitochondrial ribosomal protein S11
+Macromolecule #65: Mitoribosomal protein us12m, mrps12
+Macromolecule #66: 28S ribosomal protein S14, mitochondrial
+Macromolecule #67: 28S ribosomal protein S15, mitochondrial
+Macromolecule #68: 28S ribosomal protein S16, mitochondrial
+Macromolecule #69: uS17m
+Macromolecule #70: 28S ribosomal protein S18c, mitochondrial isoform 1
+Macromolecule #71: 28S ribosomal protein S21, mitochondrial
+Macromolecule #72: unknown
+Macromolecule #73: Mitochondrial ribosomal protein S22
+Macromolecule #74: Mitochondrial ribosomal protein S23
+Macromolecule #75: Interferon alpha-inducible protein 6
+Macromolecule #76: 28S ribosomal protein S26, mitochondrial
+Macromolecule #77: Mitochondrial ribosomal protein S27
+Macromolecule #78: 28S ribosomal protein S28, mitochondrial
+Macromolecule #79: Death associated protein 3
+Macromolecule #80: 28S ribosomal protein S31, mitochondrial
+Macromolecule #81: Mitochondrial ribosomal protein S33
+Macromolecule #82: Mitochondrial ribosomal protein S34
+Macromolecule #83: 28S ribosomal protein S35, mitochondrial isoform 1
+Macromolecule #84: Coiled-coil-helix-coiled-coil-helix domain containing 1
+Macromolecule #85: Aurora kinase A interacting protein 1
+Macromolecule #86: Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain...
+Macromolecule #87: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #88: Mitochondrial ribosomal protein L12
+Macromolecule #8: CP tRNAPhe
+Macromolecule #52: 12S rRNA
+Macromolecule #54: tRNA (P/E)
+Macromolecule #55: mRNA
+Macromolecule #56: 16S rRNA
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: ZINC ION
+Macromolecule #91: SPERMINE
+Macromolecule #92: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #93: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #94: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15545 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |