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Yorodumi- EMDB-16545: Structure of human mitochondrial CCA-adding enzyme in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16545 | |||||||||
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Title | Structure of human mitochondrial CCA-adding enzyme 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 5'-3' RNA polymerase activity / CCA tRNA nucleotidyltransferase activity / 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 ...5'-3' RNA polymerase activity / CCA tRNA nucleotidyltransferase activity / 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 / tRNA (guanosine(9)-N1)-methyltransferase activity / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-end processing / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / tRNA 3'-terminal CCA addition / 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 / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / bile acid biosynthetic process / : / positive regulation of mitochondrial translation / steroid catabolic process / tRNA processing in the nucleus / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / rescue of stalled ribosome / mitochondrion organization / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 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_16545.map.gz | 206.8 MB | EMDB map data format | |
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Header (meta data) | emd-16545-v30.xml emd-16545.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_16545.png | 62.9 KB | ||
Filedesc metadata | emd-16545.cif.gz | 7.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16545 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16545 | HTTPS FTP |
-Related structure data
Related structure data | 8cbmMC 8cbkC 8cblC 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_16545.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 CCA-adding enzyme in complex with mitochondri...
Entire | Name: Human mitochondrial CCA-adding enzyme in complex with mitochondrial pre-tRNAIle |
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Components |
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-Supramolecule #1: Human mitochondrial CCA-adding enzyme in complex with mitochondri...
Supramolecule | Name: Human mitochondrial CCA-adding enzyme in complex with mitochondrial pre-tRNAIle type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 270 KDa |
-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: 26.947021 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAAACRSVKG LVAVITGGAS GLGLATAERL VGQGASAVLL DLPNSGGEAQ AKKLGNNCVF APADVTSEKD VQTALALAKG KFGRVDVAV NCAGIAVASK TYNLKKGQTH TLEDFQRVLD VNLMGTFNVI RLVAGEMGQN EPDQGGQRGV IINTASVAAF E GQVGQAAY ...String: MAAACRSVKG LVAVITGGAS GLGLATAERL VGQGASAVLL DLPNSGGEAQ AKKLGNNCVF APADVTSEKD VQTALALAKG KFGRVDVAV NCAGIAVASK TYNLKKGQTH TLEDFQRVLD VNLMGTFNVI RLVAGEMGQN EPDQGGQRGV IINTASVAAF E GQVGQAAY SASKGGIVGM TLPIARDLAP IGIRVMTIAP GLFGTPLLTS LPEKVCNFLA SQVPFPSRLG DPAEYAHLVQ AI IENPFLN GEVIRLDGAI RMQP UniProtKB: 3-hydroxyacyl-CoA dehydrogenase type-2 |
-Macromolecule #2: CCA tRNA nucleotidyltransferase 1, mitochondrial
Macromolecule | Name: CCA tRNA nucleotidyltransferase 1, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: CCA tRNA nucleotidyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.989277 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TEGLKSLTEL FVKENHELRI AGGAVRDLLN GVKPQDIDFA TTATPTQMKE MFQSAGIRMI NNRGEKHGTI TARLHEENFE ITTLRIDVT TDGRHAEVEF TTDWQKDAER RDLTINSMFL GFDGTLFDYF NGYEDLKNKK VRFVGHAKQR IQEDYLRILR Y FRFYGRIV ...String: TEGLKSLTEL FVKENHELRI AGGAVRDLLN GVKPQDIDFA TTATPTQMKE MFQSAGIRMI NNRGEKHGTI TARLHEENFE ITTLRIDVT TDGRHAEVEF TTDWQKDAER RDLTINSMFL GFDGTLFDYF NGYEDLKNKK VRFVGHAKQR IQEDYLRILR Y FRFYGRIV DKPGDHDPET LEAIAENAKG LAGISGERIW VELKKILVGN HVNHLIHLIY DLDVAPYIGL PANASLEEFD KV SKNVDGF SPKPVTLLAS LFKVQDDVTK LDLRLKIAKE EKNLGLFIVK NRKDLIKATD SSDPLKPYQD FIIDSREPDA TTR VCELLK YQGEHCLLKE MQQWSIPPFP VSGHDIRKVG ISSGKEIGAL LQQLREQWKK SGYQMEKDEL LSYIKKT UniProtKB: CCA tRNA nucleotidyltransferase 1, mitochondrial |
-Macromolecule #3: tRNA methyltransferase 10 homolog C
Macromolecule | Name: tRNA methyltransferase 10 homolog C / type: protein_or_peptide / ID: 3 / 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: 48.007793 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHSSG VDLGTENLYF QSMSSKIPAV TYPKNESTPP SEELELDKWK TTMKSSVQEE CVSTISSSKD EDPLAATREF IEMWRLLGR EVPEHITEEE LKTLMECVSN TAKKKYLKYL YTKEKVKKAR QIKKEMKAAA REEAKNIKLL ETTEEDKQKN F LFLRLWDR ...String: MHHHHHHSSG VDLGTENLYF QSMSSKIPAV TYPKNESTPP SEELELDKWK TTMKSSVQEE CVSTISSSKD EDPLAATREF IEMWRLLGR EVPEHITEEE LKTLMECVSN TAKKKYLKYL YTKEKVKKAR QIKKEMKAAA REEAKNIKLL ETTEEDKQKN F LFLRLWDR NMDIAMGWKG AQAMQFGQPL VFDMAYENYM KRKELQNTVS QLLESEGWNR RNVDPFHIYF CNLKIDGALH RE LVKRYQE KWDKLLLTST EKSHVDLFPK DSIIYLTADS PNVMTTFRHD KVYVIGSFVD KSMQPGTSLA KAKRLNLATE CLP LDKYLQ WEIGNKNLTL DQMIRILLCL KNNGNWQEAL QFVPKRKHTG FLEISQHSQE FINRLKKAKT AENLYFQSHH HHHH DYKDD DDK UniProtKB: tRNA methyltransferase 10 homolog C |
-Macromolecule #4: Mitochondrial Precursor tRNA-Ile(0,0)
Macromolecule | Name: Mitochondrial Precursor tRNA-Ile(0,0) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.138164 KDa |
Sequence | String: GGAAAUAUGU CUGAUAAAAG AGUUACUUUG AUAGAGUAAA UAAUAGGAGC UUAAACCCCC UUAUUUCCA |
-Macromolecule #5: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Macromolecule #6: CYTIDINE-5'-DIPHOSPHATE
Macromolecule | Name: CYTIDINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: CDP |
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Molecular weight | Theoretical: 403.176 Da |
Chemical component information | ChemComp-CDP: |
-Macromolecule #7: S-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAH |
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Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ChemComp-SAH: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 8 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final 3D classification | Software - Name: cryoSPARC |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 25554 |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL / Overall B value: 60.7 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-8cbm: |