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- EMDB-16544: Structure of human mitochondrial RNase Z in complex with mitochon... -

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Entry
Database: EMDB / ID: EMD-16544
TitleStructure of human mitochondrial RNase Z in complex with mitochondrial pre-tRNA-His(0,Ser)
Map data
Sample
  • Complex: Human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(0,Ser)
    • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
    • Protein or peptide: tRNA methyltransferase 10 homolog C
    • RNA: Mitochondrial Precursor tRNA-His(0,Ser)
  • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsRNA maturation / RNA modification / mitochondrial tRNA / RNA methyltransferase / MRPP1 / MRPP2 / MRPP3 / RNA binding protein / m6A / RNA binding / RNA recognition
Function / homology
Function and homology information


tRNase Z / mitochondrial tRNA processing / tRNA-specific ribonuclease activity / mitochondrial RNA 5'-end 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 / mitochondrial tRNA methylation ...tRNase Z / mitochondrial tRNA processing / tRNA-specific ribonuclease activity / mitochondrial RNA 5'-end 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 / mitochondrial tRNA methylation / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / 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 / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / 3'-tRNA processing endoribonuclease activity / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / tRNA 3'-end processing / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / 3-hydroxyacyl-CoA dehydrogenase activity / tRNA decay / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / bile acid biosynthetic process / testosterone dehydrogenase (NAD+) activity / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / positive regulation of mitochondrial translation / tRNA processing in the nucleus / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / RNA endonuclease activity / 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 / cytosol / cytoplasm
Similarity search - Function
tRNase Z endonuclease / : / tRNase Z endonuclease / 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. / Beta-lactamase superfamily domain / tRNA methyltransferase TRMD/TRM10-type domain ...tRNase Z endonuclease / : / tRNase Z endonuclease / 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. / Beta-lactamase superfamily domain / 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. / Metallo-beta-lactamase / Short-chain dehydrogenase/reductase SDR / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
tRNA methyltransferase 10 homolog C / 3-hydroxyacyl-CoA dehydrogenase type-2 / Zinc phosphodiesterase ELAC protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsMEYNIER V / HARDWICK S / CATALA M / ROSKE J / OERUM S / CHIRGADZE D / BARRAUD P / YU W / LUISI B / TISNE C
Funding support France, 1 items
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, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16544.png

Downloads & links

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Map

FileDownload / File: emd_16544.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.65 Å/pix.
x 480 pix.
= 312.96 Å		0.65 Å/pix.
x 480 pix.
= 312.96 Å		0.65 Å/pix.
x 480 pix.
= 312.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-22.209468999999999 - 36.491726
Average (Standard dev.)-0.0028050686 (±1.1342918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 312.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human mitochondrial RNase P in complex with mitochondrial pre-tRN...

EntireName: Human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(0,Ser)
Components
  • Complex: Human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(0,Ser)
    • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
    • Protein or peptide: tRNA methyltransferase 10 homolog C
    • RNA: Mitochondrial Precursor tRNA-His(0,Ser)
  • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: Human mitochondrial RNase P in complex with mitochondrial pre-tRN...

SupramoleculeName: Human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(0,Ser)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: 3-hydroxyacyl-CoA dehydrogenase type-2

MacromoleculeName: 3-hydroxyacyl-CoA dehydrogenase type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: 3-hydroxyacyl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.947021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Zinc phosphodiesterase ELAC protein 2

MacromoleculeName: Zinc phosphodiesterase ELAC protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNase Z
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.281047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWALCSLLRS AAGRTMSQGR TISQAPARRE RPRKDPLRHL RTREKRGPSG CSGGPNTVYL QVVAAGSRDS GAALYVFSEF NRYLFNCGE GVQRLMQEHK LKVARLDNIF LTRMHWSNVG GLSGMILTLK ETGLPKCVLS GPPQLEKYLE AIKIFSGPLK G IELAVRPH ...String:
MWALCSLLRS AAGRTMSQGR TISQAPARRE RPRKDPLRHL RTREKRGPSG CSGGPNTVYL QVVAAGSRDS GAALYVFSEF NRYLFNCGE GVQRLMQEHK LKVARLDNIF LTRMHWSNVG GLSGMILTLK ETGLPKCVLS GPPQLEKYLE AIKIFSGPLK G IELAVRPH SAPEYEDETM TVYQIPIHSE QRRGKHQPWQ SPERPLSRLS PERSSDSESN ENEPHLPHGV SQRRGVRDSS LV VAFICKL HLKRGNFLVL KAKEMGLPVG TAAIAPIIAA VKDGKSITHE GREILAEELC TPPDPGAAFV VVECPDESFI QPI CENATF QRYQGKADAP VALVVHMAPA SVLVDSRYQQ WMERFGPDTQ HLVLNENCAS VHNLRSHKIQ TQLNLIHPDI FPLL TSFRC KKEGPTLSVP MVQGECLLKY QLRPRREWQR DAIITCNPEE FIVEALQLPN FQQSVQEYRR SAQDGPAPAE KRSQY PEII FLGTGSAIPM KIRNVSATLV NISPDTSLLL DCGEGTFGQL CRHYGDQVDR VLGTLAAVFV SHLAADHHTG LPSILL QRE RALASLGKPL HPLLVVAPNQ LKAWLQQYHN QCQEVLHHIS MIPAKCLQEG AEISSPAVER LISSLLRTCD LEEFQTC LV RHCKHAFGCA LVHTSGWKVV YSGDTMPCEA LVRMGKDATL LIHEATLEDG LEEEAVEKTH STTSQAISVG MRMNAEFI M LNHFSQRYAK VPLFSPNFSE KVGVAFDHMK VCFGDFPTMP KLIPPLKALF AGDIEEMEER REKRELRQVR AALLSRELA GGLEDGEPQQ KRAHTEEPQA KKVRAQ

UniProtKB: Zinc phosphodiesterase ELAC protein 2

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Macromolecule #3: tRNA methyltransferase 10 homolog C

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.007793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #4: Mitochondrial Precursor tRNA-His(0,Ser)

MacromoleculeName: Mitochondrial Precursor tRNA-His(0,Ser) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.867301 KDa
SequenceString:
GUAAAUAUAG UUUAACCAAA ACAUCAGAUU GUGAAUCUGA CAACAGAGGC UUACGACCCC UUAUUUACCG AGAAAGCUCA CAAGAACUG CUAACUCAUG CCCCCAUGUC UAACAACAUG GCUUUCUCA

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Macromolecule #5: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO32-Amino-2-hydroxymethyl-propane-1,3-diol
100.0 mMNaClSodium chloride
1.0 mMC9H15O6PTCEP
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 3 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7onu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74166
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Target criteria: Cross-correllation coefficient
Output model

PDB-8cbl:
Structure of human mitochondrial RNase Z in complex with mitochondrial pre-tRNA-His(0,Ser)

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