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- EMDB-51230: Human mitochondrial RNase Z with tRNA-His-CCA, SDR5C1/TRMT10C focus -

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Basic information

Entry
Database: EMDB / ID: EMD-51230
TitleHuman mitochondrial RNase Z with tRNA-His-CCA, SDR5C1/TRMT10C focus
Map dataHuman mitochondrial RNAseZ with tRNA-His-CCA, TRMT10C/SDR5C1/tRNA focused map
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
    • Complex: mt-tRNA-His
      • RNA: mt-tRNA-His-CCA
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRNAseZ / ELAC2 / mitochondria / tRNA / RNA BINDING PROTEIN
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 / 3-hydroxyacyl-CoA dehydrogenase / L-isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / testosterone dehydrogenase (NAD+) activity / bile acid biosynthetic process / positive regulation of mitochondrial translation / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Branched-chain amino acid catabolism / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / 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 / plasma membrane / cytoplasm
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
tRNA methyltransferase 10 homolog C / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 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
DepositionAug 1, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51230.png

Downloads & links

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Map

FileDownload / File: emd_51230.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, TRMT10C/SDR5C1/tRNA focused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 600 pix.
= 420.18 Å		0.7 Å/pix.
x 600 pix.
= 420.18 Å		0.7 Å/pix.
x 600 pix.
= 420.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7003 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.018384244 - 0.050685126
Average (Standard dev.)0.000010136569 (±0.0004326994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 420.18 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51230_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human mitochondrial RNAseZ with tRNA-His-CCA, TRMT10C/SDR5C1/tRNA focused half...

Fileemd_51230_half_map_1.map
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, TRMT10C/SDR5C1/tRNA focused half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human mitochondrial RNAseZ with tRNA-His-CCA, TRMT10C/SDR5C1/tRNA focused half...

Fileemd_51230_half_map_2.map
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, TRMT10C/SDR5C1/tRNA focused half map 2
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
    • Complex: mt-tRNA-His
      • RNA: mt-tRNA-His-CCA
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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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-#3
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: RNAseZ

SupramoleculeName: RNAseZ / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
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 #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 #4: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 293773
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 modelPDB ID:

7onu


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9gch:
Human mitochondrial RNase Z with tRNA-His-CCA, SDR5C1/TRMT10C focus

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