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Yorodumi- EMDB-16895: 28S mammalian mitochondrial small ribosomal subunit with mtRF1 an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16895 | ||||||||||||
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Title | 28S mammalian mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA | ||||||||||||
Map data | 28S mammalian mitochondrial small 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 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 / translation release factor activity / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon specific ...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 / translation release factor activity / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon specific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial ribosome / organelle membrane / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / nuclear membrane / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / mRNA binding / synapse / nucleolus / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_16895.map.gz | 450.9 MB | EMDB map data format | |
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Header (meta data) | emd-16895-v30.xml emd-16895.xml | 65.9 KB 65.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16895_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_16895.png | 200.8 KB | ||
Filedesc metadata | emd-16895.cif.gz | 15.9 KB | ||
Others | emd_16895_half_map_1.map.gz emd_16895_half_map_2.map.gz | 443 MB 443 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16895 | HTTPS FTP |
-Validation report
Summary document | emd_16895_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_16895_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_16895_validation.xml.gz | 26 KB | Display | |
Data in CIF | emd_16895_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16895 | HTTPS FTP |
-Related structure data
Related structure data | 8oipMC 8oinC 8oiqC 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_16895.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 28S mammalian mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA | ||||||||||||||||||||
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_16895_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_16895_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 28S mammalian mitochondrial small ribosomal subunit with mtRF1, m...
+Supramolecule #1: 28S mammalian mitochondrial small ribosomal subunit with mtRF1, m...
+Macromolecule #1: 39S ribosomal protein L19, mitochondrial
+Macromolecule #2: bL31m
+Macromolecule #4: 28S ribosomal protein S35, mitochondrial isoform 1
+Macromolecule #5: Mitochondrial ribosomal protein S24
+Macromolecule #6: Aurora kinase A interacting protein 1
+Macromolecule #7: bS6m,Mitochondrial ribosomal protein S6
+Macromolecule #8: Mitochondrial ribosomal protein S7
+Macromolecule #10: Mitochondrial ribosomal protein S10
+Macromolecule #12: Mitochondrial ribosomal protein S12
+Macromolecule #13: Mitochondrial ribosomal protein S14
+Macromolecule #14: 28S ribosomal protein S15, mitochondrial
+Macromolecule #15: 28S ribosomal protein S16, mitochondrial
+Macromolecule #16: uS17m
+Macromolecule #17: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #18: Mitochondrial ribosomal protein S18C
+Macromolecule #19: 28S ribosomal protein S21, mitochondrial
+Macromolecule #20: Mitochondrial ribosomal protein S22
+Macromolecule #21: mS23
+Macromolecule #22: Mitochondrial ribosomal protein S25
+Macromolecule #23: Mitochondrial ribosomal protein S26
+Macromolecule #24: Mitochondrial ribosomal protein S27
+Macromolecule #25: Mitoribosomal protein ms28, mrps28
+Macromolecule #26: Death associated protein 3
+Macromolecule #27: 28S ribosomal protein S31, mitochondrial
+Macromolecule #28: Mitochondrial ribosomal protein S33
+Macromolecule #29: Peptide chain release factor 1, mitochondrial
+Macromolecule #30: Mitochondrial ribosomal protein S2
+Macromolecule #31: Coiled-coil-helix-coiled-coil-helix domain containing 1
+Macromolecule #32: 28S ribosomal protein S5, mitochondrial isoform X2
+Macromolecule #33: mS39
+Macromolecule #34: uS9m
+Macromolecule #35: Mitochondrial ribosomal protein S11
+Macromolecule #36: Mitochondrial ribosomal protein S34
+Macromolecule #3: 12S rRNA
+Macromolecule #9: P-site Met-tRNA(fMet)
+Macromolecule #11: mRNA
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: SPERMINE
+Macromolecule #39: SPERMIDINE
+Macromolecule #40: POTASSIUM ION
+Macromolecule #41: ZINC ION
+Macromolecule #42: FE-S-O HYBRID CLUSTER
+Macromolecule #43: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #44: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #45: water
-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 small 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-8oip: |