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- EMDB-13002: Structure of human mitochondrial RNase P in complex with mitochon... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13002 | |||||||||||||||||||||
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Title | Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr | |||||||||||||||||||||
![]() | Composite map used for real space refinement. | |||||||||||||||||||||
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![]() | RNA Processing / Mitochondria / Gene Expression / Transcription / Translation / RNA BINDING PROTEIN | |||||||||||||||||||||
Function / homology | ![]() 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+) / ribonuclease P / 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 / 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 | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||||||||
![]() | Bhatta A / Dienemann C | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of RNA processing by human mitochondrial RNase P. Authors: Arjun Bhatta / Christian Dienemann / Patrick Cramer / Hauke S Hillen / ![]() Abstract: Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In ...Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria. | |||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 228.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 43.7 KB 43.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 14.2 KB 14.2 KB | Display Display | ![]() |
Images | ![]() | 107.8 KB | ||
Masks | ![]() ![]() ![]() ![]() | 244.1 MB 244.1 MB 244.1 MB 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 7.8 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 194.1 MB 230.1 MB 194.1 MB 2.3 MB 15.8 MB 226.8 MB 226.8 MB 226.8 MB 230.1 MB 226.8 MB 193.9 MB 193.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7onuMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map used for real space refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Additional map: Half map 1 for focused refinement map.
+Additional map: Post-processed map4.
+Additional map: Half map 2 for focused refinement map.
+Additional map: MRPP3-Focused refinement map.
+Additional map: Global refinement post-processed map (Map 1).
+Additional map: Half map 2 for map3.
+Additional map: Half map 2 for map4.
+Additional map: Half map 1 for map4.
+Additional map: Post-processed map3.
+Additional map: Half map 1 for map3.
+Half map: #2
+Half map: #1
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Sample components
-Entire : Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate
Entire | Name: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate |
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Components |
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-Supramolecule #1: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate
Supramolecule | Name: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 254 KDa |
-Supramolecule #2: Human mitochondrial RNase P complex with precursor mitochondrial ...
Supramolecule | Name: Human mitochondrial RNase P complex with precursor mitochondrial tRNA-Tyr type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 26.947021 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: Mitochondrial ribonuclease P catalytic subunit
Macromolecule | Name: Mitochondrial ribonuclease P catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 62.458379 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SNAFSLKTMS PQNTKATNLI AKARYLRKDE GSNKQVYSVP HFFLAGAAKE RSQMNSQTED HALAPVRNTI QLPTQPLNSE EWDKLKEDL KENTGKTSFE SWIISQMAGC HSSIDVAKSL LAWVAAKNNG IVSYDLLVKY LYLCVFHMQT SEVIDVFEIM K ARYKTLEP ...String: SNAFSLKTMS PQNTKATNLI AKARYLRKDE GSNKQVYSVP HFFLAGAAKE RSQMNSQTED HALAPVRNTI QLPTQPLNSE EWDKLKEDL KENTGKTSFE SWIISQMAGC HSSIDVAKSL LAWVAAKNNG IVSYDLLVKY LYLCVFHMQT SEVIDVFEIM K ARYKTLEP RGYSLLIRGL IHSDRWREAL LLLEDIKKVI TPSKKNYNDC IQGALLHQDV NTAWNLYQEL LGHDIVPMLE TL KAFFDFG KDIKDDNYSN KLLDILSYLR NNQLYPGESF AHSIKTWFES VPGKQWKGQF TTVRKSGQCS GCGKTIESIQ LSP EEYECL KGKIMRDVID GGDQYRKTTP QELKRFENFI KSRPPFDVVI DGLNVAKMFP KVRESQLLLN VVSQLAKRNL RLLV LGRKH MLRRSSQWSR DEMEEVQKQA SCFFADDISE DDPFLLYATL HSGNHCRFIT RDLMRDHKAC LPDAKTQRLF FKWQQ GHQL AIVNRFPGSK LTFQRILSYD TVVQTTGDSW HIPYDEDLVE RCSCEVPTKW LCLHQKT UniProtKB: Mitochondrial ribonuclease P catalytic subunit |
-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: ![]() |
Molecular weight | Theoretical: 42.942477 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SNAMSSKIPA VTYPKNESTP PSEELELDKW KTTMKSSVQE ECVSTISSSK DEDPLAATRE FIEMWRLLGR EVPEHITEEE LKTLMECVS NTAKKKYLKY LYTKEKVKKA RQIKKEMKAA AREEAKNIKL LETTEEDKQK NFLFLRLWDR NMDIAMGWKG A QAMQFGQP ...String: SNAMSSKIPA VTYPKNESTP PSEELELDKW KTTMKSSVQE ECVSTISSSK DEDPLAATRE FIEMWRLLGR EVPEHITEEE LKTLMECVS NTAKKKYLKY LYTKEKVKKA RQIKKEMKAA AREEAKNIKL LETTEEDKQK NFLFLRLWDR NMDIAMGWKG A QAMQFGQP LVFDMAYENY MKRKELQNTV SQLLESEGWN RRNVDPFHIY FCNLKIDGAL HRELVKRYQE KWDKLLLTST EK SHVDLFP KDSIIYLTAD SPNVMTTFRH DKVYVIGSFV DKSMQPGTSL AKAKRLNLAT ECLPLDKYLQ WEIGNKNLTL DQM IRILLC LKNNGNWQEA LQFVPKRKHT GFLEISQHSQ EFINRLKKAK T UniProtKB: tRNA methyltransferase 10 homolog C |
-Macromolecule #4: Mitochondrial Precursor tRNA-Tyr
Macromolecule | Name: Mitochondrial Precursor tRNA-Tyr / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41.490605 KDa |
Sequence | String: GAGAAUAGUC AACGGUCGGC GAACAUCAGU GGGGGUGAGG UAAAAUGGCU GAGUGAAGCA UUGGACUGUA AAUCUAAAGA CAGGGGUUA GGCCUCUUUU UACCAGCUCC GAGGUGAUUU UCAAGCUCG |
-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: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |