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Yorodumi- EMDB-16547: Structure of human mitochondrial MRPP1-MRPP2 in complex with mito... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16547 | |||||||||
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Title | Structure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile | |||||||||
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 / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / 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+) / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / 3-hydroxyacyl-CoA 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 / 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 / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_16547.map.gz | 98.1 MB | EMDB map data format | |
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Header (meta data) | emd-16547-v30.xml emd-16547.xml | 21 KB 21 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16547_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_16547.png | 62.2 KB | ||
Filedesc metadata | emd-16547.cif.gz | 6.8 KB | ||
Others | emd_16547_half_map_1.map.gz emd_16547_half_map_2.map.gz | 98.5 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16547 | HTTPS FTP |
-Related structure data
Related structure data | 8cboMC 8cbkC 8cblC 8cbmC 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_16547.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.723 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16547_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16547_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre...
Entire | Name: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIle |
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Components |
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-Supramolecule #1: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre...
Supramolecule | Name: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIle type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 170 KDa |
-Supramolecule #2: Human mitochondrial MRPP1-MRPP2
Supramolecule | Name: Human mitochondrial MRPP1-MRPP2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Mitochondrial pre-tRNAIle
Supramolecule | Name: Mitochondrial pre-tRNAIle / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 3-hydroxyacyl-CoA dehydrogenase type-2
Macromolecule | Name: 3-hydroxyacyl-CoA dehydrogenase type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: 3-hydroxyacyl-CoA dehydrogenase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.342254 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SVKGLVAVIT GGASGLGLAT AERLVGQGAS AVLLDLPNSG GEAQAKKLGN NCVFAPADVT SEKDVQTALA LAKGKFGRVD VAVNCAGIA VASKTYNLKK GQTHTLEDFQ RVLDVNLMGT FNVIRLVAGE MGQNEPDQGG QRGVIINTAS VAAFEGQVGQ A AYSASKGG ...String: SVKGLVAVIT GGASGLGLAT AERLVGQGAS AVLLDLPNSG GEAQAKKLGN NCVFAPADVT SEKDVQTALA LAKGKFGRVD VAVNCAGIA VASKTYNLKK GQTHTLEDFQ RVLDVNLMGT FNVIRLVAGE MGQNEPDQGG QRGVIINTAS VAAFEGQVGQ A AYSASKGG IVGMTLPIAR DLAPIGIRVM TIAPGLFGTP LLTSLPEKVC NFLASQVPFP SRLGDPAEYA HLVQAIIENP FL NGEVIRL DGAIRMQP UniProtKB: 3-hydroxyacyl-CoA dehydrogenase type-2 |
-Macromolecule #2: tRNA methyltransferase 10 homolog C
Macromolecule | Name: tRNA methyltransferase 10 homolog C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Transferring one-carbon groups; Methyltransferases |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.857826 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KNFLFLRLWD RNMDIAMGWK GAQAMQFGQP LVFDMAYENY MKRKELQNTV SQLLESEGWN RRNVDPFHIY FCNLKIDGAL HRELVKRYQ EKWDKLLLTS TEKSHVDLFP KDSIIYLTAD SPNVMTTFRH DKVYVIGSFV DKSMQPGTSL AKAKRLNLAT E CLPLDKYL ...String: KNFLFLRLWD RNMDIAMGWK GAQAMQFGQP LVFDMAYENY MKRKELQNTV SQLLESEGWN RRNVDPFHIY FCNLKIDGAL HRELVKRYQ EKWDKLLLTS TEKSHVDLFP KDSIIYLTAD SPNVMTTFRH DKVYVIGSFV DKSMQPGTSL AKAKRLNLAT E CLPLDKYL QWEIGNKNLT LDQMIRILLC LKNNGNWQEA LQFVPKRKHT GFL UniProtKB: tRNA methyltransferase 10 homolog C |
-Macromolecule #3: Mitochondrial Precursor tRNA-Ile(5,4)
Macromolecule | Name: Mitochondrial Precursor tRNA-Ile(5,4) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.118934 KDa |
Sequence | String: GGGUAAGAAA UAUGUCUGAU AAAAGAGUUA CUUUGAUAGA GUAAAUAAUA GGAGCUUAAA CCCCCUUAUU UCUAGGAC |
-Macromolecule #4: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Macromolecule #5: S-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAH |
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Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ChemComp-SAH: |
-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: 40.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL / Overall B value: 133.7 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-8cbo: |