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Yorodumi- EMDB-13562: Assembly intermediate of human mitochondrial ribosome large subun... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13562 | ||||||||||||
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Title | Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP) | ||||||||||||
Map data | Oversampled combined map of local-masked refined maps with sharpening and local-resolution filtering | ||||||||||||
Sample |
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Keywords | Small subunit / mitochondrion / biogenesis / maturation / RIBOSOME | ||||||||||||
Function / homology | Function and homology information negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / mRNA binding / nucleotide binding / calcium ion binding / synapse / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | ||||||||||||
Authors | Itoh Y / Khawaja A | ||||||||||||
Funding support | European Union, 3 items
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Citation | Journal: Nature / Year: 2022 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. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13562.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-13562-v30.xml emd-13562.xml | 81.6 KB 81.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13562_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_13562.png | 127.8 KB | ||
Masks | emd_13562_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-13562.cif.gz | 17.2 KB | ||
Others | emd_13562_additional_1.map.gz emd_13562_half_map_1.map.gz emd_13562_half_map_2.map.gz | 425.5 MB 384.5 MB 384.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13562 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13562 | HTTPS FTP |
-Validation report
Summary document | emd_13562_validation.pdf.gz | 988.8 KB | Display | EMDB validaton report |
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Full document | emd_13562_full_validation.pdf.gz | 988.4 KB | Display | |
Data in XML | emd_13562_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | emd_13562_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13562 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13562 | HTTPS FTP |
-Related structure data
Related structure data | 7po4MC 7pntC 7pnuC 7pnvC 7pnwC 7pnxC 7pnyC 7pnzC 7po0C 7po1C 7po2C 7po3C 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_13562.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 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.5625 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13562_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_13562_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: Half map of the overall refinement
File | emd_13562_half_map_1.map | ||||||||||||
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Annotation | Half map of the overall refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of the overall refinement
File | emd_13562_half_map_2.map | ||||||||||||
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Annotation | Half map of the overall refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Assembly intermediate of the large subunit of human mitochondrial...
+Supramolecule #1: Assembly intermediate of the large subunit of human mitochondrial...
+Macromolecule #1: 16SrRNA
+Macromolecule #2: tRNAVal
+Macromolecule #3: 39S ribosomal protein L2, mitochondrial
+Macromolecule #4: 39S ribosomal protein L3, mitochondrial
+Macromolecule #5: 39S ribosomal protein L4, mitochondrial
+Macromolecule #6: 39S ribosomal protein L9, mitochondrial
+Macromolecule #7: 39S ribosomal protein L10, mitochondrial
+Macromolecule #8: 39S ribosomal protein L11, mitochondrial
+Macromolecule #9: 39S ribosomal protein L13, mitochondrial
+Macromolecule #10: 39S ribosomal protein L14, mitochondrial
+Macromolecule #11: 39S ribosomal protein L15, mitochondrial
+Macromolecule #12: 39S ribosomal protein L16, mitochondrial
+Macromolecule #13: 39S ribosomal protein L17, mitochondrial
+Macromolecule #14: 39S ribosomal protein L18, mitochondrial
+Macromolecule #15: 39S ribosomal protein L19, mitochondrial
+Macromolecule #16: 39S ribosomal protein L20, mitochondrial
+Macromolecule #17: 39S ribosomal protein L21, mitochondrial
+Macromolecule #18: 39S ribosomal protein L22, mitochondrial
+Macromolecule #19: 39S ribosomal protein L23, mitochondrial
+Macromolecule #20: 39S ribosomal protein L24, mitochondrial
+Macromolecule #21: 39S ribosomal protein L27, mitochondrial
+Macromolecule #22: 39S ribosomal protein L28, mitochondrial
+Macromolecule #23: 39S ribosomal protein L47, mitochondrial
+Macromolecule #24: 39S ribosomal protein L30, mitochondrial
+Macromolecule #25: 39S ribosomal protein L32, mitochondrial
+Macromolecule #26: 39S ribosomal protein L33, mitochondrial
+Macromolecule #27: 39S ribosomal protein L34, mitochondrial
+Macromolecule #28: 39S ribosomal protein L35, mitochondrial
+Macromolecule #29: 39S ribosomal protein L37, mitochondrial
+Macromolecule #30: 39S ribosomal protein L38, mitochondrial
+Macromolecule #31: 39S ribosomal protein L39, mitochondrial
+Macromolecule #32: 39S ribosomal protein L40, mitochondrial
+Macromolecule #33: 39S ribosomal protein L41, mitochondrial
+Macromolecule #34: 39S ribosomal protein L42, mitochondrial
+Macromolecule #35: 39S ribosomal protein L43, mitochondrial
+Macromolecule #36: 39S ribosomal protein L44, mitochondrial
+Macromolecule #37: 39S ribosomal protein L45, mitochondrial
+Macromolecule #38: 39S ribosomal protein L46, mitochondrial
+Macromolecule #39: 39S ribosomal protein L48, mitochondrial
+Macromolecule #40: 39S ribosomal protein L49, mitochondrial
+Macromolecule #41: 39S ribosomal protein L50, mitochondrial
+Macromolecule #42: 39S ribosomal protein L51, mitochondrial
+Macromolecule #43: 39S ribosomal protein L52, mitochondrial
+Macromolecule #44: 39S ribosomal protein L53, mitochondrial
+Macromolecule #45: 39S ribosomal protein L54, mitochondrial
+Macromolecule #46: 39S ribosomal protein L55, mitochondrial
+Macromolecule #47: Ribosomal protein 63, mitochondrial
+Macromolecule #48: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #49: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #50: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #51: 39S ribosomal protein S30, mitochondrial
+Macromolecule #52: 39S ribosomal protein L12, mitochondrial
+Macromolecule #53: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #54: MIEF1 upstream open reading frame protein
+Macromolecule #55: Acyl carrier protein, mitochondrial
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: POTASSIUM ION
+Macromolecule #58: ZINC ION
+Macromolecule #59: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #60: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+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: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / 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: 20583 / Average exposure time: 5.0 sec. / Average electron dose: 31.0 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: 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 |