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Yorodumi- EMDB-16896: 39S mammalian mitochondrial large ribosomal subunit with mtRF1 an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16896 | ||||||||||||
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Title | 39S mammalian mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA | ||||||||||||
Map data | 39S mammalian mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA | ||||||||||||
Sample |
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Keywords | mammalian mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon / RIBOSOME | ||||||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / mitochondrial translational elongation / mitochondrial translational termination / translation release factor activity, codon nonspecific / microprocessor complex / translation release factor activity, codon specific / ribonuclease III activity / Mitochondrial protein degradation ...Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / mitochondrial translational elongation / mitochondrial translational termination / translation release factor activity, codon nonspecific / microprocessor complex / translation release factor activity, codon specific / ribonuclease III activity / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / organelle membrane / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / double-stranded RNA binding / cell junction / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / mRNA binding / synapse / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Saurer M / Leibundgut M / Scaiola A / Schoenhut T / Ban N | ||||||||||||
Funding support | Switzerland, European Union, 3 items
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Citation | Journal: Science / Year: 2023 Title: Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / ...Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / David Gatfield / Aleksandra Filipovska / Nenad Ban / Abstract: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the ...The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16896.map.gz | 450.7 MB | EMDB map data format | |
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Header (meta data) | emd-16896-v30.xml emd-16896.xml | 86.9 KB 86.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16896_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_16896.png | 195.1 KB | ||
Filedesc metadata | emd-16896.cif.gz | 18.9 KB | ||
Others | emd_16896_half_map_1.map.gz emd_16896_half_map_2.map.gz | 443 MB 443 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16896 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16896 | HTTPS FTP |
-Validation report
Summary document | emd_16896_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_16896_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_16896_validation.xml.gz | 26 KB | Display | |
Data in CIF | emd_16896_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16896 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16896 | HTTPS FTP |
-Related structure data
Related structure data | 8oiqMC 8oinC 8oipC 8oirC 8oisC 8oitC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16896.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 39S mammalian mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_16896_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_16896_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 39S mammalian mitochondrial ribosome with mtRF1 and P-site tRNAMet
+Supramolecule #1: 39S mammalian mitochondrial ribosome with mtRF1 and P-site tRNAMet
+Macromolecule #1: Mitochondrial ribosomal protein L12
+Macromolecule #5: Large ribosomal subunit protein uL22m
+Macromolecule #6: 39S ribosomal protein L23, mitochondrial
+Macromolecule #7: uL24m
+Macromolecule #8: 39S ribosomal protein L27, mitochondrial
+Macromolecule #9: Mitochondrial ribosomal protein L28
+Macromolecule #10: Mitochondrial ribosomal protein L47
+Macromolecule #11: Large ribosomal subunit protein uL30m
+Macromolecule #12: Mitochondrial ribosomal protein L32
+Macromolecule #13: Large ribosomal subunit protein bL33m
+Macromolecule #14: Large ribosomal subunit protein bL34m
+Macromolecule #15: 39S ribosomal protein L35, mitochondrial
+Macromolecule #16: Mitochondrial ribosomal protein L2
+Macromolecule #17: ICT1
+Macromolecule #18: Mitochondrial ribosomal protein L4
+Macromolecule #19: Mitochondrial ribosomal protein L9
+Macromolecule #20: Mitochondrial ribosomal protein L10
+Macromolecule #21: Mitochondrial ribosomal protein L11
+Macromolecule #22: 39S ribosomal protein L13, mitochondrial
+Macromolecule #23: Mitochondrial ribosomal protein L14
+Macromolecule #24: 39S ribosomal protein L15, mitochondrial
+Macromolecule #25: uL16m
+Macromolecule #26: bL17m
+Macromolecule #27: Mitochondrial ribosomal protein L18
+Macromolecule #28: 39S ribosomal protein L19, mitochondrial
+Macromolecule #29: Mitochondrial ribosomal protein L20
+Macromolecule #30: Mitochondrial ribosomal protein L21
+Macromolecule #31: 39S ribosomal protein L52, mitochondrial
+Macromolecule #32: Mitochondrial ribosomal protein L53
+Macromolecule #33: mL54
+Macromolecule #34: Mitochondrial ribosomal protein L55
+Macromolecule #35: Mitochondrial ribosomal protein L57
+Macromolecule #36: mL62 (ICT1)
+Macromolecule #37: mL64
+Macromolecule #38: Mitochondrial ribosomal protein S18A
+Macromolecule #39: 39S ribosomal protein S30, mitochondrial
+Macromolecule #40: 39S ribosomal protein L1, mitochondrial
+Macromolecule #41: Ribosomal protein
+Macromolecule #42: Mitochondrial ribosomal protein L37
+Macromolecule #43: Mitochondrial ribosomal protein L38
+Macromolecule #44: Mitochondrial ribosomal protein L39
+Macromolecule #45: Mitochondrial ribosomal protein L40
+Macromolecule #46: 39S ribosomal protein L41, mitochondrial
+Macromolecule #47: mL42
+Macromolecule #48: Large ribosomal subunit protein mL43
+Macromolecule #49: mL44
+Macromolecule #50: Mitochondrial ribosomal protein L45
+Macromolecule #51: Mitochondrial ribosomal protein L46
+Macromolecule #52: 39S ribosomal protein L48, mitochondrial
+Macromolecule #53: 39S ribosomal protein L49, mitochondrial
+Macromolecule #54: Mitochondrial ribosomal protein L50
+Macromolecule #55: Large ribosomal subunit protein mL51
+Macromolecule #57: Peptide chain release factor 1, mitochondrial
+Macromolecule #2: E-site tRNA
+Macromolecule #3: 16S rRNA
+Macromolecule #4: CP Phe-tRNA
+Macromolecule #56: P-site Met-tRNA(fMet)
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: POTASSIUM ION
+Macromolecule #60: PHENYLALANINE
+Macromolecule #61: ZINC ION
+Macromolecule #62: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #63: N-FORMYLMETHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 20mM HEPES-KOH pH=7.5, 100mM KCl, 20mM MgCl2, ~1% sucrose (from mtRF1 storage buffer) | ||||||||||||
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | In vitro reconstituted complex (55S). Focused refinement on large subunit. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6973 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||||||||
Output model | PDB-8oiq: |