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- PDB-7onu: Structure of human mitochondrial RNase P in complex with mitochon... -

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Basic information

Entry
Database: PDB / ID: 7onu
TitleStructure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr
Components
  • (Mitochondrial ...) x 2
  • 3-hydroxyacyl-CoA dehydrogenase type-2
  • tRNA methyltransferase 10 homolog C
KeywordsRNA BINDING PROTEIN / RNA Processing / Mitochondria / Gene Expression / Transcription / Translation
Function / homology
Function and homology information


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 / mitochondrial tRNA methylation / tRNA (adenine9-N1)-methyltransferase / mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / tRNA (adenine(9)-N1)-methyltransferase activity ...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 / mitochondrial tRNA methylation / tRNA (adenine9-N1)-methyltransferase / mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / tRNA (adenine(9)-N1)-methyltransferase activity / 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 / tRNA modification in the mitochondrion / rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase (NAD+) activity / C21-steroid hormone metabolic process / tRNA methyltransferase complex / ribonuclease P / 3-hydroxyacyl-CoA dehydrogenase / L-isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / bile acid biosynthetic process / testosterone dehydrogenase (NAD+) activity / positive regulation of mitochondrial translation / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Branched-chain amino acid catabolism / ribonuclease P activity / tRNA 5'-leader removal / estrogen metabolic process / fatty acid beta-oxidation / androgen metabolic process / mitochondrial nucleoid / 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 / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Mitochondrial ribonuclease P catalytic subunit / Protein-only RNase P, C-terminal / Protein-only RNase P / 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 TrmD ...Mitochondrial ribonuclease P catalytic subunit / Protein-only RNase P, C-terminal / Protein-only RNase P / 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 TrmD / 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 / RNA / RNA (> 10) / RNA (> 100) / 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: 3 Å
AuthorsBhatta, A. / Dienemann, C. / Cramer, P. / Hillen, H.S.
Funding support Germany, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB1190 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)CHROMATRANS 693023 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2021
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
DepositionMay 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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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-Tyr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,42313
Polymers254,6807
Non-polymers2,7436
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, In-vitro reconstitution of the complex from recombinant subunits and gel filtration performed by us and others (Oerum et al. 2018) supports mtRNase P complex assembly.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33180 Å2
ΔGint-237 kcal/mol
Surface area74250 Å2
MethodPISA

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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 / Production host: Escherichia coli BL21 (bacteria)
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: 42942.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT10C, MRPP1, RG9MTD1 / Production host: Escherichia coli BL21 (bacteria)
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: 62458.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRORP, KIAA0391, MRPP3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15091, ribonuclease P
#4: RNA chain Mitochondrial Precursor tRNA-Tyr


Mass: 41490.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)

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Non-polymers , 3 types, 6 molecules

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


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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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

Component
IDNameTypeEntity IDParent-IDSource
1Human mitochondrial RNase P complex with precursor tRNA-Tyr substrateCOMPLEX#1-#40RECOMBINANT
2Human mitochondrial RNase P complex with precursor mitochondrial tRNA-TyrCOMPLEX#1-#41RECOMBINANT
Molecular weightValue: 0.254 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mmol/LSodium ChlorideNaCl1
240 mmol/LNa-HEPES (Sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonate)C8H17N2O4SNa1
30.25 mmol/LEthylenediaminetetraacetic acid disodium saltC10H16N2O8Na1
42 mmol/mLDithiothreitolC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4RELION3CTF correctionUsed for CTF correction after 3D reconstruction.
5Warp1.0.9CTF correctionUsed for initial per-micrograph CTF estimation.
11cryoSPARC2.11.2initial Euler assignment
12RELION3final Euler assignment
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 6150677
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88081 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415510
ELECTRON MICROSCOPYf_angle_d0.94121339
ELECTRON MICROSCOPYf_dihedral_angle_d13.9336028
ELECTRON MICROSCOPYf_chiral_restr0.042490
ELECTRON MICROSCOPYf_plane_restr0.0052501

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