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Yorodumi- EMDB-12569: 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12569 | |||||||||
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Title | 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) | |||||||||
Map data | map filtered to 3.9A instead of FSC weighting in Relion | |||||||||
Sample |
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Keywords | Ribosome / Mitochondria / tRNA(E*) / TRANSLATION | |||||||||
Function / homology | Function and homology information Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly ...Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / ribonuclease III activity / microprocessor complex / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / organelle membrane / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / double-stranded RNA binding / large ribosomal subunit / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / nuclear membrane / cytosolic large ribosomal subunit / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / synapse / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Kummer E / Schubert K | |||||||||
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_12569.map.gz | 392.7 MB | EMDB map data format | |
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Header (meta data) | emd-12569-v30.xml emd-12569.xml | 113.9 KB 113.9 KB | Display Display | EMDB header |
Images | emd_12569.png | 71.1 KB | ||
Masks | emd_12569_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-12569.cif.gz | 22 KB | ||
Others | emd_12569_additional_1.map.gz emd_12569_additional_2.map.gz emd_12569_additional_3.map.gz emd_12569_half_map_1.map.gz emd_12569_half_map_2.map.gz | 49.3 MB 1019 MB 337.2 MB 340 MB 339.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12569 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12569 | HTTPS FTP |
-Validation report
Summary document | emd_12569_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_12569_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_12569_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_12569_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12569 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12569 | HTTPS FTP |
-Related structure data
Related structure data | 7nsjMC 7nqhC 7nqlC 7nshC 7nsiC 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_12569.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 3.9A 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_12569_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: masked and postprocessed map (map filtered to 3.9A...
File | emd_12569_additional_1.map | ||||||||||||
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Annotation | masked and postprocessed map (map filtered to 3.9A instead of FSC weighting in Relion) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 5x supersampled map
File | emd_12569_additional_2.map | ||||||||||||
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Annotation | 5x supersampled map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: full map from 3D gold-standard refinement
File | emd_12569_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_12569_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12569_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)
+Supramolecule #1: 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)
+Macromolecule #1: Mitochondrial ribosomal protein L27
+Macromolecule #2: Mitochondrial ribosomal protein L28
+Macromolecule #3: Mitochondrial ribosomal protein L47
+Macromolecule #4: uL30m
+Macromolecule #5: bL31m
+Macromolecule #6: bL32m
+Macromolecule #7: bL33m
+Macromolecule #9: Mitochondrial ribosomal protein L34
+Macromolecule #10: uL2m
+Macromolecule #11: ICT1
+Macromolecule #12: Mitochondrial ribosomal protein L4
+Macromolecule #13: Mitochondrial ribosomal protein L9
+Macromolecule #14: Mitochondrial ribosomal protein L10
+Macromolecule #15: Mitochondrial ribosomal protein L11
+Macromolecule #16: uL13m
+Macromolecule #17: uL14m
+Macromolecule #18: uL15m
+Macromolecule #19: uL16m
+Macromolecule #20: bL17m
+Macromolecule #21: Mitochondrial ribosomal protein L18
+Macromolecule #22: Mitochondrial ribosomal protein L19
+Macromolecule #23: Mitochondrial ribosomal protein L20
+Macromolecule #24: Mitochondrial ribosomal protein L21
+Macromolecule #25: uL22m
+Macromolecule #26: uL23m
+Macromolecule #27: uL24m
+Macromolecule #28: Mitochondrial ribosomal protein L37
+Macromolecule #29: Mitochondrial ribosomal protein L38
+Macromolecule #30: Mitochondrial ribosomal protein L39
+Macromolecule #31: Mitochondrial ribosomal protein L40
+Macromolecule #32: Mitochondrial ribosomal protein L41
+Macromolecule #33: mL42
+Macromolecule #34: Mitochondrial ribosomal protein L43
+Macromolecule #35: mL44
+Macromolecule #36: Mitochondrial ribosomal protein L35
+Macromolecule #37: Mitochondrial ribosomal protein L45
+Macromolecule #38: Mitochondrial ribosomal protein L46
+Macromolecule #39: 39S ribosomal protein L48, mitochondrial
+Macromolecule #40: Mrpl34
+Macromolecule #41: Mitochondrial ribosomal protein L50
+Macromolecule #42: Mitochondrial ribosomal protein L51
+Macromolecule #43: mL52
+Macromolecule #44: mL53
+Macromolecule #45: mL54
+Macromolecule #46: Mitochondrial ribosomal protein L57
+Macromolecule #47: mL62 (ICT1)
+Macromolecule #48: mL64
+Macromolecule #49: 39S ribosomal protein S30, mitochondrial
+Macromolecule #50: Mitochondrial ribosomal protein S18A
+Macromolecule #52: Ribosomal protein
+Macromolecule #54: Mitochondrial ribosomal protein S2
+Macromolecule #55: Mitochondrial ribosomal protein S24
+Macromolecule #56: 28S ribosomal protein S5, mitochondrial isoform X2
+Macromolecule #57: bS6m
+Macromolecule #58: Mitochondrial ribosomal protein S7
+Macromolecule #59: uS9m
+Macromolecule #60: Mitochondrial ribosomal protein S10
+Macromolecule #61: uS11m
+Macromolecule #62: Mitochondrial ribosomal protein S12
+Macromolecule #63: Mitochondrial ribosomal protein S14
+Macromolecule #64: uS15m
+Macromolecule #65: 28S ribosomal protein S16, mitochondrial
+Macromolecule #66: uS17m
+Macromolecule #67: Mitochondrial ribosomal protein S18C
+Macromolecule #68: bS21m
+Macromolecule #69: unknown
+Macromolecule #70: Mitochondrial ribosomal protein S22
+Macromolecule #71: mS23
+Macromolecule #72: Mitochondrial ribosomal protein S25
+Macromolecule #73: Mitochondrial ribosomal protein S26
+Macromolecule #74: Mitochondrial ribosomal protein S27
+Macromolecule #75: Mitoribosomal protein ms28, mrps28
+Macromolecule #76: Death associated protein 3
+Macromolecule #77: 28S ribosomal protein S31, mitochondrial
+Macromolecule #78: mS33
+Macromolecule #79: mS34
+Macromolecule #80: Mitochondrial ribosomal protein S35
+Macromolecule #81: mS37
+Macromolecule #82: Aurora kinase A interacting protein 1
+Macromolecule #83: Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain...
+Macromolecule #84: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #85: Mitochondrial ribosomal protein L12
+Macromolecule #8: CP tRNAPhe
+Macromolecule #51: 12S rRNA
+Macromolecule #53: 16S rRNA
+Macromolecule #86: tRNA(P/P) and tRNA(E*)
+Macromolecule #87: mRNA
+Macromolecule #88: MAGNESIUM ION
+Macromolecule #89: ZINC ION
+Macromolecule #90: SPERMINE
+Macromolecule #91: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #92: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #93: 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
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26001 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |