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- PDB-8cbk: Structure of human mitochondrial RNase P in complex with mitochon... -

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Basic information

Entry
Database: PDB / ID: 8cbk
TitleStructure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(5,Ser)
Components
  • (Mitochondrial ...) x 2
  • 3-hydroxyacyl-CoA dehydrogenase type-2
  • tRNA methyltransferase 10 homolog C
KeywordsRNA BINDING PROTEIN / RNA maturation / RNA modification / mitochondrial tRNA / RNA methyltransferase / MRPP1 / MRPP2 / MRPP3 / 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 / 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 / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / ribonuclease P / 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 / : / steroid catabolic process / 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 / mitochondrion organization / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitochondrial ribonuclease P catalytic subunit / tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / Protein-only RNase P, C-terminal / Protein-only RNase P / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase ...Mitochondrial ribonuclease P catalytic subunit / tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / Protein-only RNase P, C-terminal / Protein-only RNase P / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Mitochondrial ribonuclease P catalytic subunit / tRNA methyltransferase 10 homolog C / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsMEYNIER, V. / HARDWICK, S. / CATALA, M. / ROSKE, J. / OERUM, S. / CHIRGADZE, D. / BARRAUD, P. / LUISI, B. / TISNE, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE07-0028 France
CitationJournal: 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
DepositionJan 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase type-2
B: 3-hydroxyacyl-CoA dehydrogenase type-2
C: 3-hydroxyacyl-CoA dehydrogenase type-2
D: 3-hydroxyacyl-CoA dehydrogenase type-2
E: Mitochondrial ribonuclease P catalytic subunit
F: tRNA methyltransferase 10 homolog C
T: Mitochondrial Precursor tRNA-His(5,Ser)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,25314
Polymers247,1257
Non-polymers3,1287
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 5 molecules ABCDF

#1: Protein
3-hydroxyacyl-CoA dehydrogenase type-2 / 17-beta-estradiol 17-dehydrogenase / 2-methyl-3-hydroxybutyryl-CoA dehydrogenase / MHBD / 3-alpha- ...17-beta-estradiol 17-dehydrogenase / 2-methyl-3-hydroxybutyryl-CoA dehydrogenase / MHBD / 3-alpha-(17-beta)-hydroxysteroid dehydrogenase (NAD(+)) / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase type II / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / 7-alpha-hydroxysteroid dehydrogenase / Endoplasmic reticulum-associated amyloid beta-peptide-binding protein / Mitochondrial ribonuclease P protein 2 / Mitochondrial RNase P protein 2 / Short chain dehydrogenase/reductase family 5C member 1 / Short-chain type dehydrogenase/reductase XH98G2 / Type II HADH


Mass: 26947.021 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B10, ERAB, HADH2, MRPP2, SCHAD, SDR5C1, XH98G2 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli)
References: UniProt: Q99714, 3-hydroxyacyl-CoA dehydrogenase, 17beta-estradiol 17-dehydrogenase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), 3-hydroxy-2-methylbutyryl-CoA dehydrogenase, ...References: UniProt: Q99714, 3-hydroxyacyl-CoA dehydrogenase, 17beta-estradiol 17-dehydrogenase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), 3-hydroxy-2-methylbutyryl-CoA dehydrogenase, 3alpha(or 20beta)-hydroxysteroid dehydrogenase, 7alpha-hydroxysteroid dehydrogenase
#3: Protein tRNA methyltransferase 10 homolog C / HBV pre-S2 trans-regulated protein 2 / Mitochondrial ribonuclease P protein 1 / Mitochondrial RNase ...HBV pre-S2 trans-regulated protein 2 / Mitochondrial ribonuclease P protein 1 / Mitochondrial RNase P protein 1 / RNA (guanine-9-)-methyltransferase domain-containing protein 1 / Renal carcinoma antigen NY-REN-49 / mRNA methyladenosine-N(1)-methyltransferase / tRNA (adenine(9)-N(1))-methyltransferase / tRNA (guanine(9)-N(1))-methyltransferase


Mass: 48007.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT10C, MRPP1, RG9MTD1 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli)
References: UniProt: Q7L0Y3, Transferases; Transferring one-carbon groups; Methyltransferases, tRNA (adenine9-N1)-methyltransferase, tRNA (guanine9-N1)-methyltransferase

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Mitochondrial ... , 2 types, 2 molecules ET

#2: Protein Mitochondrial ribonuclease P catalytic subunit / Mitochondrial ribonuclease P protein 3 / Mitochondrial RNase P protein 3 / Protein only RNase P ...Mitochondrial ribonuclease P protein 3 / Mitochondrial RNase P protein 3 / Protein only RNase P catalytic subunit


Mass: 61564.430 Da / Num. of mol.: 1 / Mutation: D479A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRORP, KIAA0391, MRPP3 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: O15091, ribonuclease P
#4: RNA chain Mitochondrial Precursor tRNA-His(5,Ser)


Mass: 29764.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: in vitro transcription vector pT7-TP(deltai) (others)

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Non-polymers , 5 types, 15 molecules

#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human mitochondrial RNase P in complex with mitochondrial pre-tRNAHis-Ser
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.269 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-Amino-2-hydroxymethyl-propane-1,3-diolC4H11NO31
2100 mMSodium chlorideNaCl1
31 mMTCEPC9H15O6P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 48.52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1Warpparticle selectionParticles axtraction
4WarpCTF correctionCTF CORRECTION
7UCSF Chimera1.11.2model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
19Coot0.8.9.1model refinement
20PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81396 / Symmetry type: POINT
Atomic model buildingB value: 70.7 / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient

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