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Open data
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Basic information
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Title | Human mitochondrial ribosome small subunit | ||||||||||||
![]() | Oversampled combined map of local-masked refined maps with sharpening and local-resolution filtering | ||||||||||||
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![]() | Small subunit / mitochondrion / RIBOSOME | ||||||||||||
Function / homology | ![]() mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation ...mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / cell junction / 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 | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||||||||
![]() | Itoh Y / Khawaja A | ||||||||||||
Funding support | European Union, 3 items
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![]() | ![]() Title: Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Authors: Yuzuru Itoh / Anas Khawaja / Ivan Laptev / Miriam Cipullo / Ilian Atanassov / Petr Sergiev / Joanna Rorbach / Alexey Amunts / ![]() ![]() ![]() Abstract: Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) ...Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 747.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 56.5 KB 56.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17 KB | Display | ![]() |
Images | ![]() | 86.8 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Filedesc metadata | ![]() | 13.3 KB | ||
Others | ![]() ![]() ![]() | 376.8 MB 338.4 MB 338.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7po3MC ![]() 7pntC ![]() 7pnuC ![]() 7pnvC ![]() 7pnwC ![]() 7pnxC ![]() 7pnyC ![]() 7pnzC ![]() 7po0C ![]() 7po1C ![]() 7po2C ![]() 7po4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Oversampled combined map of local-masked refined maps with sharpening and local-resolution filtering | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Combined map of local-masked refined maps without sharpening
File | emd_13561_additional_1.map | ||||||||||||
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Annotation | Combined map of local-masked refined maps without sharpening | ||||||||||||
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-Half map: Half map of the overall refinement
File | emd_13561_half_map_1.map | ||||||||||||
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Annotation | Half map of the overall refinement | ||||||||||||
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Density Histograms |
-Half map: Half map of the overall refinement
File | emd_13561_half_map_2.map | ||||||||||||
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Annotation | Half map of the overall refinement | ||||||||||||
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Sample components
+Entire : Small subunit of human mitochondrial ribosome
+Supramolecule #1: Small subunit of human mitochondrial ribosome
+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: MAGNESIUM ION
+Macromolecule #33: POTASSIUM ION
+Macromolecule #34: ZINC ION
+Macromolecule #35: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #36: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #37: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #38: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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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: 20583 / Average exposure time: 5.0 sec. / Average electron dose: 31.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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: 1.0 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |