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Yorodumi- EMDB-13170: Human mitochondrial ribosome small subunit in complex with IF3, G... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13170 | |||||||||
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Title | Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin | |||||||||
Map data | Oversampled combined map of local-masked refined maps with sharpening and local-resolution filtering. | |||||||||
Sample |
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Keywords | Initiation factor 3 / translation / antibiotic / streptomycin / RIBOSOME | |||||||||
Function / homology | Function and homology information mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / ribosome disassembly ...mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / ribosome disassembly / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / translation initiation factor activity / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / cell junction / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / cell population proliferation / tRNA binding / rRNA binding / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Itoh Y / Khawaja A / Rorbach J / Amunts A | |||||||||
Funding support | Sweden, 2 items
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Citation | Journal: Elife / Year: 2022 Title: Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules. Authors: Yuzuru Itoh / Vivek Singh / Anas Khawaja / Andreas Naschberger / Minh Duc Nguyen / Joanna Rorbach / Alexey Amunts / Abstract: The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was ...The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13170.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-13170-v30.xml emd-13170.xml | 64.4 KB 64.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13170_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_13170.png | 84.9 KB | ||
Masks | emd_13170_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-13170.cif.gz | 14.5 KB | ||
Others | emd_13170_additional_1.map.gz emd_13170_half_map_1.map.gz emd_13170_half_map_2.map.gz | 371.7 MB 337.9 MB 337.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13170 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13170 | HTTPS FTP |
-Related structure data
Related structure data | 7p2eMC M: atomic model generated by this map C: citing same article (ref.) |
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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_13170.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Oversampled combined map of local-masked refined maps with sharpening and local-resolution filtering. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.55333 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13170_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Combined map of local-masked refined maps without sharpening
File | emd_13170_additional_1.map | ||||||||||||
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Annotation | Combined map of local-masked refined maps without sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall refinement
File | emd_13170_half_map_1.map | ||||||||||||
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Annotation | Overall refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall refinement
File | emd_13170_half_map_2.map | ||||||||||||
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Annotation | Overall refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Small subunit of human mitochondrial ribosome in complex with ini...
+Supramolecule #1: Small subunit of human mitochondrial ribosome in complex with ini...
+Supramolecule #2: Small subunit of human mitochondrial ribosome in complex
+Supramolecule #3: Translation initiation factor IF-3, mitochondrial
+Macromolecule #1: 12S mitochondrial rRNA
+Macromolecule #2: 28S ribosomal protein S2, mitochondrial
+Macromolecule #3: 28S ribosomal protein S24, mitochondrial
+Macromolecule #4: 28S ribosomal protein S5, mitochondrial
+Macromolecule #5: 28S ribosomal protein S6, mitochondrial
+Macromolecule #6: 28S ribosomal protein S7, mitochondrial
+Macromolecule #7: 28S ribosomal protein S9, mitochondrial
+Macromolecule #8: 28S ribosomal protein S10, mitochondrial
+Macromolecule #9: 28S ribosomal protein S11, mitochondrial
+Macromolecule #10: 28S ribosomal protein S12, mitochondrial
+Macromolecule #11: 28S ribosomal protein S14, mitochondrial
+Macromolecule #12: 28S ribosomal protein S15, mitochondrial
+Macromolecule #13: 28S ribosomal protein S16, mitochondrial
+Macromolecule #14: 28S ribosomal protein S17, mitochondrial
+Macromolecule #15: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #16: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #17: 28S ribosomal protein S21, mitochondrial
+Macromolecule #18: 28S ribosomal protein S22, mitochondrial
+Macromolecule #19: 28S ribosomal protein S23, mitochondrial
+Macromolecule #20: 28S ribosomal protein S25, mitochondrial
+Macromolecule #21: 28S ribosomal protein S26, mitochondrial
+Macromolecule #22: 28S ribosomal protein S27, mitochondrial
+Macromolecule #23: 28S ribosomal protein S28, mitochondrial
+Macromolecule #24: 28S ribosomal protein S29, mitochondrial
+Macromolecule #25: 28S ribosomal protein S31, mitochondrial
+Macromolecule #26: 28S ribosomal protein S33, mitochondrial
+Macromolecule #27: 28S ribosomal protein S34, mitochondrial
+Macromolecule #28: 28S ribosomal protein S35, mitochondrial
+Macromolecule #29: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #30: Aurora kinase A-interacting protein
+Macromolecule #31: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #32: Translation initiation factor IF-3, mitochondrial
+Macromolecule #33: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #34: SPERMINE
+Macromolecule #35: [(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[...
+Macromolecule #36: POTASSIUM ION
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ZINC ION
+Macromolecule #39: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #40: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #41: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #42: 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:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number real images: 31773 / Average exposure time: 4.0 sec. / Average electron dose: 30.0 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: 4.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |