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- EMDB-50052: Human mitochondrial RNase Z with tRNA-His-CCA -

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Basic information

Entry
Database: EMDB / ID: EMD-50052
TitleHuman mitochondrial RNase Z with tRNA-His-CCA
Map dataHuman mitochondrial RNAseZ with tRNA-His-CCA, composite map, locscale2
Sample
  • Complex: RNAseZ with mt-tRNA-His
    • Complex: RNAseZ
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
      • Protein or peptide: tRNA methyltransferase 10 homolog C
      • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
    • Complex: mt-tRNA-His
      • RNA: mt-tRNA-His-CCA
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
KeywordsRNase Z / ELAC2 / mitochondria / tRNA / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNase Z / 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 ...tRNase Z / 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 / 3'-tRNA processing endoribonuclease activity / tRNA methyltransferase complex / tRNA 3'-end processing / 3-hydroxyacyl-CoA dehydrogenase / tRNA-specific ribonuclease activity / L-isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / tRNA decay / : / 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 / tRNA processing in the nucleus / estrogen metabolic process / fatty acid beta-oxidation / androgen metabolic process / mitochondrial nucleoid / RNA endonuclease activity / 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 / 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 TrmD / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Short-chain dehydrogenase/reductase SDR / 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: 2.96 Å
AuthorsValentin Gese G / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO J / Year: 2024
Title: Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex.
Authors: Genís Valentín Gesé / B Martin Hällberg /
Abstract: Maturation of human mitochondrial tRNA is essential for cellular energy production, yet the underlying mechanisms remain only partially understood. Here, we present several cryo-EM structures of the ...Maturation of human mitochondrial tRNA is essential for cellular energy production, yet the underlying mechanisms remain only partially understood. Here, we present several cryo-EM structures of the mitochondrial RNase Z complex (ELAC2/SDR5C1/TRMT10C) bound to different maturation states of mitochondrial tRNA, showing the molecular basis for tRNA-substrate selection and catalysis. Our structural insights provide a molecular rationale for the 5'-to-3' tRNA processing order in mitochondria, the 3'-CCA antideterminant effect, and the basis for sequence-independent recognition of mitochondrial tRNA substrates. Furthermore, our study links mutations in ELAC2 to clinically relevant mitochondrial diseases, offering a deeper understanding of the molecular defects contributing to these conditions.
History
DepositionApr 9, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50052.png

Downloads & links

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Map

FileDownload / File: emd_50052.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, composite map, locscale2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 600 pix.
= 420.16 Å		0.7 Å/pix.
x 600 pix.
= 420.16 Å		0.7 Å/pix.
x 600 pix.
= 420.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.70027 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.49913058 - 39.811349999999997
Average (Standard dev.)0.012490379 (±0.33768877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 420.16022 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50052_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNAseZ with mt-tRNA-His

EntireName: RNAseZ with mt-tRNA-His
Components
  • Complex: RNAseZ with mt-tRNA-His
    • Complex: RNAseZ
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
      • Protein or peptide: tRNA methyltransferase 10 homolog C
      • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
    • Complex: mt-tRNA-His
      • RNA: mt-tRNA-His-CCA
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: RNAseZ with mt-tRNA-His

SupramoleculeName: RNAseZ with mt-tRNA-His / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: RNAseZ

SupramoleculeName: RNAseZ / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: mt-tRNA-His

SupramoleculeName: mt-tRNA-His / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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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: tRNA methyltransferase 10 homolog C

MacromoleculeName: tRNA methyltransferase 10 homolog C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.055281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSVQEECV STISSSKDED PLAATREFIE MWRLLGREVP EHITEEELKT LMECVSNTAK KKYLKYLYTK EKVKKARQIK KEMKAAARE EAKNIKLLET TEEDKQKNFL FLRLWDRNMD IAMGWKGAQA MQFGQPLVFD MAYENYMKRK ELQNTVSQLL E SEGWNRRN ...String:
MKSSVQEECV STISSSKDED PLAATREFIE MWRLLGREVP EHITEEELKT LMECVSNTAK KKYLKYLYTK EKVKKARQIK KEMKAAARE EAKNIKLLET TEEDKQKNFL FLRLWDRNMD IAMGWKGAQA MQFGQPLVFD MAYENYMKRK ELQNTVSQLL E SEGWNRRN VDPFHIYFCN LKIDGALHRE LVKRYQEKWD KLLLTSTEKS HVDLFPKDSI IYLTADSPNV MTTFRHDKVY VI GSFVDKS MQPGTSLAKA KRLNLATECL PLDKYLQWEI GNKNLTLDQM IRILLCLKNN GNWQEALQFV PKRKHTGFLE ISQ HSQEFI NRLKKAKTAE NLYFQSHHHH HHDYKDDDDK

UniProtKB: tRNA methyltransferase 10 homolog C

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Macromolecule #4: Zinc phosphodiesterase ELAC protein 2

MacromoleculeName: Zinc phosphodiesterase ELAC protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNase Z
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.142328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SRPRKDPLRH LRTREKRGPS GCSGGPNTVY LQVVAAGSRD SGAALYVFSE FNRYLFNCGE GVQRLMQEHK LKVARLDNIF LTRMHWSNV GGLSGMILTL KETGLPKCVL SGPPQLEKYL EAIKIFSGPL KGIELAVRPH SAPEYEDETM TVYQIPIHSE Q RRGKHQPW ...String:
SRPRKDPLRH LRTREKRGPS GCSGGPNTVY LQVVAAGSRD SGAALYVFSE FNRYLFNCGE GVQRLMQEHK LKVARLDNIF LTRMHWSNV GGLSGMILTL KETGLPKCVL SGPPQLEKYL EAIKIFSGPL KGIELAVRPH SAPEYEDETM TVYQIPIHSE Q RRGKHQPW QSPERPLSRL SPERSSDSES NENEPHLPHG VSQRRGVRDS SLVVAFICKL HLKRGNFLVL KAKEMGLPVG TA AIAPIIA AVKDGKSITH EGREILAEEL CTPPDPGAAF VVVECPDESF IQPICENATF QRYQGKADAP VALVVHMAPA SVL VDSRYQ QWMERFGPDT QHLVLNENCA SVHNLRSHKI QTQLNLIHPD IFPLLTSFRC KKEGPTLSVP MVQGECLLKY QLRP RREWQ RDAIITCNPE EFIVEALQLP NFQQSVQEYR RSAQDGPAPA EKRSQYPEII FLGTGSAIPM KIRNVSATLV NISPD TSLL LDCGEGTFGQ LCRHYGDQVD RVLGTLAAVF VSHLHADHHT GLPSILLQRE RALASLGKPL HPLLVVAPNQ LKAWLQ QYH NQCQEVLHHI SMIPAKCLQE GAEISSPAVE RLISSLLRTC DLEEFQTCLV RHCKHAFGCA LVHTSGWKVV YSGDTMP CE ALVRMGKDAT LLIHEATLED GLEEEAVEKT HSTTSQAISV GMRMNAEFIM LNHFSQRYAK VPLFSPNFSE KVGVAFDH M KVCFGDFPTM PKLIPPLKAL FAGDIEEMEE RREKRELRQV RAALLSRELA GGLEDGEPQQ KRAHTEEPQA KKVRAQ

UniProtKB: Zinc phosphodiesterase ELAC protein 2

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Macromolecule #3: mt-tRNA-His-CCA

MacromoleculeName: mt-tRNA-His-CCA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.626486 KDa
SequenceString:
UAAAUAUAGU UUAACCAAAA CAUCAGAUUG UGAAUCUGAC AACAGAGGCU UACGACCCCU UAUUUACCCC A

GENBANK: GENBANK: LC530717.1

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Macromolecule #5: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4773315
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4436
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta-1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7onu

source_name: PDB, initial_model_type: experimental model

bq52

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ey2:
Human mitochondrial RNase Z with tRNA-His-CCA

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