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Yorodumi- EMDB-71802: In Situ Structure of the Human Mitoribosome Large Subunit 39S in ... -
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| Title | In Situ Structure of the Human Mitoribosome Large Subunit 39S in Complex with EF-Tu | |||||||||
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Keywords | mitochondria / mitoribosome / inner membrane / RIBOSOME | |||||||||
| Function / homology | Function and homology informationmitochondrial protein quality control / protein insertion into mitochondrial inner membrane from matrix / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / membrane insertase activity / negative regulation of mitochondrial translation / SARS-CoV-2 modulates autophagy / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation ...mitochondrial protein quality control / protein insertion into mitochondrial inner membrane from matrix / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / membrane insertase activity / negative regulation of mitochondrial translation / SARS-CoV-2 modulates autophagy / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / protein lipoylation / positive regulation of mitochondrial translation / Complex I biogenesis / Respiratory electron transport / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / negative regulation of ATP-dependent activity / Mitochondrial ribosome-associated quality control / mitochondrial translational elongation / Mitochondrial translation elongation / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / mitochondrial proton-transporting ATP synthase complex assembly / Mitochondrial translation termination / mitochondrial fission / iron-sulfur cluster assembly complex / translation release factor activity / mitochondrial large ribosomal subunit binding / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial [2Fe-2S] assembly complex / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / protein-synthesizing GTPase / [2Fe-2S] cluster assembly / mitochondrial translation / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / mitochondrial nucleoid / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / translational elongation / respiratory chain complex I / anatomical structure morphogenesis / translation elongation factor activity / RNA processing / Mitochondrial protein degradation / rescue of stalled cytosolic ribosome / fatty acid binding / aerobic respiration / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / protein tetramerization / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / mitochondrial outer membrane / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / calcium ion binding / positive regulation of DNA-templated transcription / GTP binding / nucleolus / structural molecule activity / magnesium ion binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Wang S / Xiong Y / Zhang Y | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2026Title: Structural basis of TACO1-mediated efficient mitochondrial translation. Authors: Shuhui Wang / Michele Brischigliaro / Yuekang Zhang / Chunxiang Wu / Wei Zheng / Antoni Barrientos / Yong Xiong / ![]() Abstract: Translation elongation is a universally conserved step in protein synthesis, relying on elongation factors that engage the ribosomal L7/L12 stalk to mediate aminoacyl-tRNA delivery, accommodation, ...Translation elongation is a universally conserved step in protein synthesis, relying on elongation factors that engage the ribosomal L7/L12 stalk to mediate aminoacyl-tRNA delivery, accommodation, and ribosomal translocation. Using in organello cryo-electron microscopy, we reveal how the mitochondrial translation accelerator TACO1 promotes efficient elongation on human mitoribosomes. TACO1 binds the mitoribosomal region typically bound by elongation factor Tu (mtEF-Tu), bridging the large and small subunits via contacts with 16S rRNA, bL12m, A-site tRNA, and uS12m. While active throughout elongation, TACO1 is especially critical when translating polyproline motifs. Its absence prolongs mtEF-Tu residence in A/T states, causes persistent mitoribosomal stalling and premature subunit dissociation. Structural analyses indicate that TACO1 competes with mtEF-Tu for mitoribosome binding, stabilizes A-site tRNA, and enhances peptidyl transfer through a mechanism distinct from EF-P and eIF5A. These findings suggest that bacterial TACO1 orthologs may serve analogous roles, highlighting an evolutionarily conserved strategy for maintaining elongation efficiency during challenging translation events. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_71802.map.gz | 212.4 MB | EMDB map data format | |
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| Header (meta data) | emd-71802-v30.xml emd-71802.xml | 84.2 KB 84.2 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_71802_fsc.xml | 15.8 KB | Display | FSC data file |
| Images | emd_71802.png | 56.3 KB | ||
| Masks | emd_71802_msk_1.map | 421.9 MB | Mask map | |
| Filedesc metadata | emd-71802.cif.gz | 17.7 KB | ||
| Others | emd_71802_additional_1.map.gz emd_71802_half_map_1.map.gz emd_71802_half_map_2.map.gz | 398.6 MB 392 MB 392 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-71802 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71802 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9praMC ![]() 9olfC ![]() 9pr4C ![]() 9prdC ![]() 9prqC ![]() 9prxC ![]() 9ps0C ![]() 9ps7C ![]() 9psiC ![]() 9psmC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_71802.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_71802_msk_1.map | ||||||||||||
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-Additional map: #1
| File | emd_71802_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_71802_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_71802_half_map_2.map | ||||||||||||
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Sample components
+Entire : mitochondria
+Supramolecule #1: mitochondria
+Macromolecule #1: 39S ribosomal protein L32, mitochondrial
+Macromolecule #2: 39S ribosomal protein L33, mitochondrial
+Macromolecule #3: 39S ribosomal protein L34, mitochondrial
+Macromolecule #4: 39S ribosomal protein L35, mitochondrial
+Macromolecule #5: 39S ribosomal protein L36, mitochondrial
+Macromolecule #6: 39S ribosomal protein L37, mitochondrial
+Macromolecule #7: 39S ribosomal protein L38, mitochondrial
+Macromolecule #8: 39S ribosomal protein L39, mitochondrial
+Macromolecule #9: 39S ribosomal protein L40, mitochondrial
+Macromolecule #10: 39S ribosomal protein L41, mitochondrial
+Macromolecule #11: 39S ribosomal protein L45, mitochondrial
+Macromolecule #12: 39S ribosomal protein L46, mitochondrial
+Macromolecule #13: 39S ribosomal protein L48, mitochondrial
+Macromolecule #14: 39S ribosomal protein L2, mitochondrial
+Macromolecule #15: 39S ribosomal protein L3, mitochondrial
+Macromolecule #16: 39S ribosomal protein L4, mitochondrial
+Macromolecule #17: 39S ribosomal protein L12, mitochondrial
+Macromolecule #18: 39S ribosomal protein L9, mitochondrial
+Macromolecule #19: 39S ribosomal protein L10, mitochondrial
+Macromolecule #20: 39S ribosomal protein L11, mitochondrial
+Macromolecule #21: Large ribosomal subunit protein uL13m
+Macromolecule #22: 39S ribosomal protein L14, mitochondrial
+Macromolecule #23: 39S ribosomal protein L15, mitochondrial
+Macromolecule #24: 39S ribosomal protein L16, mitochondrial
+Macromolecule #25: 39S ribosomal protein L17, mitochondrial
+Macromolecule #26: 39S ribosomal protein L18, mitochondrial
+Macromolecule #27: 39S ribosomal protein L19, mitochondrial
+Macromolecule #28: 39S ribosomal protein L20, mitochondrial
+Macromolecule #29: 39S ribosomal protein L21, mitochondrial
+Macromolecule #30: 39S ribosomal protein L22, mitochondrial
+Macromolecule #31: 39S ribosomal protein L23, mitochondrial
+Macromolecule #32: 39S ribosomal protein L24, mitochondrial
+Macromolecule #33: 39S ribosomal protein L27, mitochondrial
+Macromolecule #34: 39S ribosomal protein L28, mitochondrial
+Macromolecule #35: 39S ribosomal protein L47, mitochondrial
+Macromolecule #36: 39S ribosomal protein L30, mitochondrial
+Macromolecule #37: 39S ribosomal protein L43, mitochondrial
+Macromolecule #38: 39S ribosomal protein L49, mitochondrial
+Macromolecule #39: 39S ribosomal protein L50, mitochondrial
+Macromolecule #40: 39S ribosomal protein L51, mitochondrial
+Macromolecule #41: 39S ribosomal protein L52, mitochondrial
+Macromolecule #42: Large ribosomal subunit protein mL53
+Macromolecule #43: 39S ribosomal protein L54, mitochondrial
+Macromolecule #44: 39S ribosomal protein L55, mitochondrial
+Macromolecule #45: Nascent polypeptide
+Macromolecule #46: Ribosomal protein 63, mitochondrial
+Macromolecule #47: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #48: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #49: Large ribosomal subunit protein uL1m
+Macromolecule #50: Elongation factor Tu, mitochondrial
+Macromolecule #52: 39S ribosomal protein L44, mitochondrial
+Macromolecule #53: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #54: 39S ribosomal protein S30, mitochondrial
+Macromolecule #55: Mitochondrial inner membrane protein OXA1L
+Macromolecule #56: 39S ribosomal protein L42, mitochondrial
+Macromolecule #57: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #58: Mitochondrial ribosome and complex I assembly factor AltMIEF1
+Macromolecule #59: Acyl carrier protein, mitochondrial
+Macromolecule #51: 16S mitochondrial rRNA
+Macromolecule #60: mitochondrial tRNAVal
+Macromolecule #61: ZINC ION
+Macromolecule #62: POTASSIUM ION
+Macromolecule #63: MAGNESIUM ION
+Macromolecule #64: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #65: SPERMIDINE
+Macromolecule #66: 1,4-DIAMINOBUTANE
+Macromolecule #67: VALINE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN


