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Yorodumi- EMDB-12567: 39S mammalian mitochondrial large ribosomal subunit with mtRRF (p... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12567 | |||||||||
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Title | 39S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosome / Mitochondria / TRANSLATION | |||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation termination / Mitochondrial protein degradation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation termination / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / ribosome disassembly / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / organelle membrane / mitochondrial translation / ribosomal large subunit binding / RNA processing / rescue of stalled ribosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell junction / large ribosomal subunit / double-stranded RNA binding / cytosolic large ribosomal subunit / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / synapse / positive regulation of DNA-templated transcription / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_12567.map.gz | 389.9 MB | EMDB map data format | |
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Header (meta data) | emd-12567-v30.xml emd-12567.xml | 87.8 KB 87.8 KB | Display Display | EMDB header |
Images | emd_12567.png | 70.2 KB | ||
Masks | emd_12567_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-12567.cif.gz | 16.6 KB | ||
Others | emd_12567_additional_1.map.gz emd_12567_additional_2.map.gz emd_12567_additional_3.map.gz emd_12567_half_map_1.map.gz emd_12567_half_map_2.map.gz | 40.3 MB 2.2 GB 337.8 MB 340.1 MB 339.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12567 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12567 | HTTPS FTP |
-Validation report
Summary document | emd_12567_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_12567_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_12567_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_12567_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12567 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12567 | HTTPS FTP |
-Related structure data
Related structure data | 7nshMC 7nqhC 7nqlC 7nsiC 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_12567.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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_12567_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: postprocessed and masked map
File | emd_12567_additional_1.map | ||||||||||||
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Annotation | postprocessed and masked map | ||||||||||||
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Density Histograms |
-Additional map: 5x supersampled map
File | emd_12567_additional_2.map | ||||||||||||
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Annotation | 5x supersampled map | ||||||||||||
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Density Histograms |
-Additional map: full map from 3D gold-standard refinement
File | emd_12567_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_12567_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12567_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 39S mammalian mitochondrial large ribosomal subunit with mtRRF (p...
+Supramolecule #1: 39S mammalian mitochondrial large ribosomal subunit with mtRRF (p...
+Supramolecule #3: mtRRF (post) and mtEFG2
+Supramolecule #2: 39S mammalian mitochondrial large ribosomal subunit
+Macromolecule #1: Mitochondrial ribosomal protein L27
+Macromolecule #2: uL24m
+Macromolecule #3: Mitochondrial ribosomal protein L37
+Macromolecule #4: Mitochondrial ribosomal protein L35
+Macromolecule #5: Mitochondrial ribosomal protein L38
+Macromolecule #6: Mitochondrial ribosomal protein L39
+Macromolecule #7: Mitochondrial ribosomal protein L40
+Macromolecule #8: Mitochondrial ribosomal protein L41
+Macromolecule #9: mL42
+Macromolecule #10: Mitochondrial ribosomal protein L43
+Macromolecule #11: mL44
+Macromolecule #12: Mitochondrial ribosomal protein L45
+Macromolecule #13: Mitochondrial ribosomal protein L46
+Macromolecule #14: 39S ribosomal protein L48, mitochondrial
+Macromolecule #15: Mrpl34
+Macromolecule #16: Mitochondrial ribosomal protein L50
+Macromolecule #17: Mitochondrial ribosomal protein L51
+Macromolecule #18: mL52
+Macromolecule #19: mL53
+Macromolecule #20: mL54
+Macromolecule #21: Mitochondrial ribosomal protein L57
+Macromolecule #22: mL62 (ICT1)
+Macromolecule #23: mL64
+Macromolecule #24: 39S ribosomal protein S30, mitochondrial
+Macromolecule #25: Mitochondrial ribosomal protein S18A
+Macromolecule #26: Mitochondrial ribosomal protein L12
+Macromolecule #27: Mitochondrial ribosomal protein L28
+Macromolecule #28: Ribosomal protein
+Macromolecule #30: Mitochondrial ribosomal protein L47
+Macromolecule #31: uL30m
+Macromolecule #32: bL31m
+Macromolecule #33: bL32m
+Macromolecule #34: bL33m
+Macromolecule #35: Mitochondrial ribosomal protein L34
+Macromolecule #37: Ribosome-releasing factor 2, mitochondrial
+Macromolecule #38: uL2m
+Macromolecule #39: Ribosome-recycling factor, mitochondrial
+Macromolecule #40: uL16m
+Macromolecule #41: ICT1
+Macromolecule #42: Mitochondrial ribosomal protein L4
+Macromolecule #43: Mitochondrial ribosomal protein L9
+Macromolecule #44: Mitochondrial ribosomal protein L10
+Macromolecule #45: Mitochondrial ribosomal protein L11
+Macromolecule #46: uL13m
+Macromolecule #47: uL14m
+Macromolecule #48: uL15m
+Macromolecule #49: bL17m
+Macromolecule #50: Mitochondrial ribosomal protein L18
+Macromolecule #51: Mitochondrial ribosomal protein L19
+Macromolecule #52: Mitochondrial ribosomal protein L20
+Macromolecule #53: Mitochondrial ribosomal protein L21
+Macromolecule #54: uL22m
+Macromolecule #55: uL23m
+Macromolecule #29: 16S rRNA
+Macromolecule #36: CP tRNAPhe
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: ZINC ION
+Macromolecule #58: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #59: SPERMINE
+Macromolecule #60: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #61: 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224731 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |