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- EMDB-19453: Human mitochondrial RNase Z complex with ELAC2-D550N catalytic mu... -

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Basic information

Entry
Database: EMDB / ID: EMD-19453
TitleHuman mitochondrial RNase Z complex with ELAC2-D550N catalytic mutant and tRNA-Tyr precursor (Composite model)
Map dataComposite map of human mitochondrial RNase Z complex with mitochondrial tRNA-Tyr precursor
Sample
  • Complex: Human mitochondrial RNase Z complex with tRNA-Tyr precursor
    • Complex: 3-hydroxyacyl-CoA dehydrogenase type-2A
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
    • Complex: Zinc phosphodiesterase ELAC protein 2
      • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
    • Complex: tRNA methyltransferase 10 homolog C
      • Protein or peptide: tRNA methyltransferase 10 homolog C
    • Complex: tRNA-Tyr precursor
      • RNA: Human mitochondrial tRNA-Tyr precursor with 3' trailer
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordstRNA processing / RNase Z / endonuclease / mitochondrial / 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 / 3-hydroxyacyl-CoA dehydrogenase 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 / testosterone dehydrogenase [NAD(P)+] activity / 17beta-estradiol 17-dehydrogenase / Branched-chain amino acid catabolism / 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 / fatty acid metabolic process / mitochondrion organization / 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: 2.93 Å
AuthorsBhatta A / Yu RD / Kuhle B / Hillen HS
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1565 Germany
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)EXC 2067/1 390729940 Germany
German Research Foundation (DFG)SFB1190 Germany
European Research Council (ERC)MitoRNA 101116869European Union
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Molecular basis of human nuclear and mitochondrial tRNA 3' processing.
Authors: Arjun Bhatta / Bernhard Kuhle / Ryan D Yu / Lucas Spanaus / Katja Ditter / Katherine E Bohnsack / Hauke S Hillen /
Abstract: Eukaryotic transfer RNA (tRNA) precursors undergo sequential processing steps to become mature tRNAs. In humans, ELAC2 carries out 3' end processing of both nucleus-encoded (nu-tRNAs) and ...Eukaryotic transfer RNA (tRNA) precursors undergo sequential processing steps to become mature tRNAs. In humans, ELAC2 carries out 3' end processing of both nucleus-encoded (nu-tRNAs) and mitochondria-encoded (mt-tRNAs) tRNAs. ELAC2 is self-sufficient for processing of nu-tRNAs but requires TRMT10C and SDR5C1 to process most mt-tRNAs. Here we show that TRMT10C and SDR5C1 specifically facilitate processing of structurally degenerate mt-tRNAs lacking the canonical elbow. Structures of ELAC2 in complex with TRMT10C, SDR5C1 and two divergent mt-tRNA substrates reveal two distinct mechanisms of pre-tRNA recognition. While canonical nu-tRNAs and mt-tRNAs are recognized by direct ELAC2-RNA interactions, processing of noncanonical mt-tRNAs depends on protein-protein interactions between ELAC2 and TRMT10C. These results provide the molecular basis for tRNA 3' processing in both the nucleus and the mitochondria and explain the organelle-specific requirement for additional factors. Moreover, they suggest that TRMT10C-SDR5C1 evolved as a mitochondrial tRNA maturation platform to compensate for the structural erosion of mt-tRNAs in bilaterian animals.
History
DepositionJan 22, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19453.png

Downloads & links

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Map

FileDownload / File: emd_19453.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of human mitochondrial RNase Z complex with mitochondrial tRNA-Tyr precursor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-13.935663 - 34.940586000000003
Average (Standard dev.)0.007941936 (±1.1341751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19453_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_19453_msk_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Global refinement map for human mitochondrial RNase Z...

Fileemd_19453_additional_1.map
AnnotationGlobal refinement map for human mitochondrial RNase Z complex with mitochondrial tRNA-Tyr precursor - Sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution-filtered global refinement map

Fileemd_19453_additional_2.map
AnnotationLocal resolution-filtered global refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution-filtered map for focused refinement around ELAC2...

Fileemd_19453_additional_6.map
AnnotationLocal resolution-filtered map for focused refinement around ELAC2 density
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Human mitochondrial RNase Z complex with tRNA-Tyr precursor

EntireName: Human mitochondrial RNase Z complex with tRNA-Tyr precursor
Components
  • Complex: Human mitochondrial RNase Z complex with tRNA-Tyr precursor
    • Complex: 3-hydroxyacyl-CoA dehydrogenase type-2A
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
    • Complex: Zinc phosphodiesterase ELAC protein 2
      • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
    • Complex: tRNA methyltransferase 10 homolog C
      • Protein or peptide: tRNA methyltransferase 10 homolog C
    • Complex: tRNA-Tyr precursor
      • RNA: Human mitochondrial tRNA-Tyr precursor with 3' trailer
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: Human mitochondrial RNase Z complex with tRNA-Tyr precursor

SupramoleculeName: Human mitochondrial RNase Z complex with tRNA-Tyr precursor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: 3-hydroxyacyl-CoA dehydrogenase type-2A

SupramoleculeName: 3-hydroxyacyl-CoA dehydrogenase type-2A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Zinc phosphodiesterase ELAC protein 2

SupramoleculeName: Zinc phosphodiesterase ELAC protein 2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: tRNA methyltransferase 10 homolog C

SupramoleculeName: tRNA methyltransferase 10 homolog C / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: tRNA-Tyr precursor

SupramoleculeName: tRNA-Tyr precursor / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
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 BL21(DE3) (bacteria)
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: 89.169336 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAPRKDPLR HLRTREKRGP SGCSGGPNTV YLQVVAAGSR DSGAALYVFS EFNRYLFNCG EGVQRLMQEH KLKVARLDNI FLTRMHWSN VGGLSGMILT LKETGLPKCV LSGPPQLEKY LEAIKIFSGP LKGIELAVRP HSAPEYEDET MTVYQIPIHS E QRRGKHQP ...String:
SNAPRKDPLR HLRTREKRGP SGCSGGPNTV YLQVVAAGSR DSGAALYVFS EFNRYLFNCG EGVQRLMQEH KLKVARLDNI FLTRMHWSN VGGLSGMILT LKETGLPKCV LSGPPQLEKY LEAIKIFSGP LKGIELAVRP HSAPEYEDET MTVYQIPIHS E QRRGKHQP WQSPERPLSR LSPERSSDSE SNENEPHLPH GVSQRRGVRD SSLVVAFICK LHLKRGNFLV LKAKEMGLPV GT AAIAPII AAVKDGKSIT HEGREILAEE LCTPPDPGAA FVVVECPDES FIQPICENAT FQRYQGKADA PVALVVHMAP ASV LVDSRY QQWMERFGPD TQHLVLNENC ASVHNLRSHK IQTQLNLIHP DIFPLLTSFR CKKEGPTLSV PMVQGECLLK YQLR PRREW QRDAIITCNP EEFIVEALQL PNFQQSVQEY RRSAQDGPAP AEKRSQYPEI IFLGTGSAIP MKIRNVSATL VNISP DTSL LLDCGEGTFG QLCRHYGDQV DRVLGTLAAV FVSHLHANHH TGLPSILLQR ERALASLGKP LHPLLVVAPN QLKAWL QQY HNQCQEVLHH ISMIPAKCLQ EGAEISSPAV ERLISSLLRT CDLEEFQTCL VRHCKHAFGC ALVHTSGWKV VYSGDTM PC EALVRMGKDA TLLIHEATLE DGLEEEAVEK THSTTSQAIS VGMRMNAEFI MLNHFSQRYA KVPLFSPNFS EKVGVAFD H MKVCFGDFPT MPKLIPPLKA LFAGDIEEME ERREKRELRQ VRAALLSREL AGGLEDGEPQ QKRAHTEEPQ AKKVRAQ

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: 37.165094 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SNAAATREFI EMWRLLGREV PEHITEEELK TLMECVSNTA KKKYLKYLYT KEKVKKARQI KKEMKAAARE EAKNIKLLET TEEDKQKNF LFLRLWDRNM DIAMGWKGAQ AMQFGQPLVF DMAYENYMKR KELQNTVSQL LESEGWNRRN VDPFHIYFCN L KIDGALHR ...String:
SNAAATREFI EMWRLLGREV PEHITEEELK TLMECVSNTA KKKYLKYLYT KEKVKKARQI KKEMKAAARE EAKNIKLLET TEEDKQKNF LFLRLWDRNM DIAMGWKGAQ AMQFGQPLVF DMAYENYMKR KELQNTVSQL LESEGWNRRN VDPFHIYFCN L KIDGALHR ELVKRYQEKW DKLLLTSTEK SHVDLFPKDS IIYLTADSPN VMTTFRHDKV YVIGSFVDKS MQPGTSLAKA KR LNLATEC LPLDKYLQWE IGNKNLTLDQ MIRILLCLKN NGNWQEALQF VPKRKHTGFL EISQHSQEFI NRLKKAKT

UniProtKB: tRNA methyltransferase 10 homolog C

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Macromolecule #4: Human mitochondrial tRNA-Tyr precursor with 3' trailer

MacromoleculeName: Human mitochondrial tRNA-Tyr precursor with 3' trailer
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.023184 KDa
SequenceString:
GGUAAAAUGG CUGAGUGAAG CAUUGGACUG UAAAUCUAAA GACAGGGGUU AGGCCUCUUU UUACCAGCUC CGAGGUGAUU UUCAAGCUC G

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 6 / 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

BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SNaHEPES sodium salt
20.0 mMNaClsodium chloride
20.0 uMZnCl2Zinc chloride
2.0 mMC4H10O2S2Dithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5987454
Details: Particles picked by neural net based picker in Warp
Startup modelType of model: EMDB MAP
EMDB ID:

13002

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 57585
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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