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- PDB-8cbo: Structure of human mitochondrial MRPP1-MRPP2 in complex with mito... -

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Entry
Database: PDB / ID: 8cbo
TitleStructure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile
Components
  • 3-hydroxyacyl-CoA dehydrogenase type-2
  • Mitochondrial Precursor tRNA-Ile(5,4)
  • 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 / 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 / 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 / plasma membrane / cytoplasm / cytosol
Similarity search - Function
tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / 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. ...tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / 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: 3.2 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

Downloads & links

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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: tRNA methyltransferase 10 homolog C
T: Mitochondrial Precursor tRNA-Ile(5,4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,38411
Polymers155,3466
Non-polymers3,0385
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#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: 26342.254 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
#2: 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: 24857.826 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
#3: RNA chain Mitochondrial Precursor tRNA-Ile(5,4)


Mass: 25118.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: 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
#5: 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
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

Component
IDNameTypeEntity IDParent-IDSource
1Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIleCOMPLEX#1-#30MULTIPLE SOURCES
2Human mitochondrial MRPP1-MRPP2COMPLEX#1-#21RECOMBINANT
3Mitochondrial pre-tRNAIleCOMPLEX#31RECOMBINANT
Molecular weightValue: 0.170 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
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: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1MotionCorr2particle selection
4CTFFIND4.1CTF correctionCTF CORRECTION
7UCSF Chimera1.11.2model fitting
9Coot0.8.9.1model refinement
10PHENIX1.20.1model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141653 / Symmetry type: POINT
Atomic model buildingB value: 133.7 / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient

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