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Yorodumi- EMDB-16543: Structure of human mitochondrial RNase P in complex with mitochon... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16543 | |||||||||
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Title | Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(5,Ser) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA maturation / RNA modification / mitochondrial tRNA / RNA methyltransferase / MRPP1 / MRPP2 / MRPP3 / RNA binding protein / m6A / RNA binding / RNA recognition | |||||||||
Function / homology | Function and homology information mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation ...mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA processing in the mitochondrion / tRNA (guanine9-N1)-methyltransferase / mitochondrial ribonuclease P complex / tRNA (guanosine(9)-N1)-methyltransferase activity / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / ribonuclease P / 3-hydroxyacyl-CoA dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / bile acid biosynthetic process / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / positive regulation of mitochondrial translation / ribonuclease P activity / tRNA 5'-leader removal / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / mRNA processing / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
Authors | MEYNIER V / HARDWICK S / CATALA M / ROSKE J / OERUM S / CHIRGADZE D / BARRAUD P / LUISI B / TISNE C | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for human mitochondrial tRNA maturation. Authors: Vincent Meynier / Steven W Hardwick / Marjorie Catala / Johann J Roske / Stephanie Oerum / Dimitri Y Chirgadze / Pierre Barraud / Wyatt W Yue / Ben F Luisi / Carine Tisné / Abstract: The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by ...The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by the mitochondrial endoribonucleases (mt-RNase), P and Z, releases all RNA species from the two RNA transcripts. The tRNAs then undergo 3'-CCA addition. In metazoan mitochondria, RNase P is a multi-enzyme assembly that comprises the endoribonuclease PRORP and a tRNA methyltransferase subcomplex. The requirement for this tRNA methyltransferase subcomplex for mt-RNase P cleavage activity, as well as the mechanisms of pre-tRNA 3'-cleavage and 3'-CCA addition, are still poorly understood. Here, we report cryo-EM structures that visualise four steps of mitochondrial tRNA maturation: 5' and 3' tRNA-end processing, methylation and 3'-CCA addition, and explain the defined sequential order of the tRNA processing steps. The methyltransferase subcomplex recognises the pre-tRNA in a distinct mode that can support tRNA-end processing and 3'-CCA addition, likely resulting from an evolutionary adaptation of mitochondrial tRNA maturation complexes to the structurally-fragile mitochondrial tRNAs. This subcomplex can also ensure a tRNA-folding quality-control checkpoint before the sequential docking of the maturation enzymes. Altogether, our study provides detailed molecular insight into RNA-transcript processing and tRNA maturation in human mitochondria. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16543.map.gz | 392 MB | EMDB map data format | |
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Header (meta data) | emd-16543-v30.xml emd-16543.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_16543.png | 69 KB | ||
Filedesc metadata | emd-16543.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16543 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16543 | HTTPS FTP |
-Validation report
Summary document | emd_16543_validation.pdf.gz | 509.8 KB | Display | EMDB validaton report |
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Full document | emd_16543_full_validation.pdf.gz | 509.4 KB | Display | |
Data in XML | emd_16543_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | emd_16543_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16543 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16543 | HTTPS FTP |
-Related structure data
Related structure data | 8cbkMC 8cblC 8cbmC 8cboC 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_16543.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: 0.652 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Human mitochondrial RNase P in complex with mitochondrial pre-tRN...
+Supramolecule #1: Human mitochondrial RNase P in complex with mitochondrial pre-tRN...
+Macromolecule #1: 3-hydroxyacyl-CoA dehydrogenase type-2
+Macromolecule #2: Mitochondrial ribonuclease P catalytic subunit
+Macromolecule #3: tRNA methyltransferase 10 homolog C
+Macromolecule #4: Mitochondrial Precursor tRNA-His(5,Ser)
+Macromolecule #5: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #6: ZINC ION
+Macromolecule #7: S-ADENOSYL-L-HOMOCYSTEINE
+Macromolecule #8: MAGNESIUM ION
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 3 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.52 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL / Overall B value: 70.7 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-8cbk: |