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

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Basic information

Entry
Database: PDB / ID: 9ey2
TitleHuman mitochondrial RNase Z with tRNA-His-CCA
Components
  • 3-hydroxyacyl-CoA dehydrogenase type-2
  • Zinc phosphodiesterase ELAC protein 2
  • mt-tRNA-His-CCA
  • tRNA methyltransferase 10 homolog C
KeywordsRNA BINDING PROTEIN / RNase Z / ELAC2 / mitochondria / tRNA
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 (NAD+) activity / tRNA decay / : / 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 / 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 / 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 / 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
GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYLMETHIONINE / : / RNA / RNA (> 10) / tRNA methyltransferase 10 homolog C / 3-hydroxyacyl-CoA dehydrogenase type-2 / Zinc phosphodiesterase ELAC protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsValentin Gese, G. / Hallberg, B.M.
Funding support1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
F: tRNA methyltransferase 10 homolog C
T: mt-tRNA-His-CCA
E: Zinc phosphodiesterase ELAC protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,66511
Polymers261,6127
Non-polymers1,0524
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 6 molecules ABCDFE

#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 (E. coli)
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
#2: 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: 42055.281 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 (E. coli)
References: UniProt: Q7L0Y3, Transferases; Transferring one-carbon groups; Methyltransferases, tRNA (adenine9-N1)-methyltransferase, tRNA (guanine9-N1)-methyltransferase
#4: Protein Zinc phosphodiesterase ELAC protein 2 / ElaC homolog protein 2 / Heredity prostate cancer protein 2 / Ribonuclease Z 2 / RNase Z 2 / tRNA 3 ...ElaC homolog protein 2 / Heredity prostate cancer protein 2 / Ribonuclease Z 2 / RNase Z 2 / tRNA 3 endonuclease 2 / tRNase Z 2


Mass: 89142.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELAC2, HPC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQ52, tRNase Z

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RNA chain , 1 types, 1 molecules T

#3: RNA chain mt-tRNA-His-CCA


Mass: 22626.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1896813685

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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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
1RNAseZ with mt-tRNA-HisCOMPLEX#1-#40MULTIPLE SOURCES
2RNAseZCOMPLEX#1-#2, #41RECOMBINANT
3mt-tRNA-HisCOMPLEX#31RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
4Warp1.0.9CTF correction
7Coot0.9.8model fitting
9PHENIX1.20.1-4487model refinement
10cryoSPARC4.3.1initial Euler assignment
11RELION5.0-beta-1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4773315
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4436 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17ONU

7onu

17ONU1PDBexperimental model
21Q9BQ522AlphaFoldin silico model
RefinementResolution: 2.96→2.96 Å / Cor.coef. Fo:Fc: 0.811 / SU B: 24.858 / SU ML: 0.401 / ESU R: 0.376
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.34984 --
obs0.34984 194874 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 45.811 Å2
Refinement stepCycle: 1 / Total: 16556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0170.01217040
ELECTRON MICROSCOPYr_bond_other_d00.01615728
ELECTRON MICROSCOPYr_angle_refined_deg0.41.82823357
ELECTRON MICROSCOPYr_angle_other_deg0.1391.74236265
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.7585.7812318
ELECTRON MICROSCOPYr_dihedral_angle_2_deg4.896592
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.353102644
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0410.2012749
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0218894
ELECTRON MICROSCOPYr_gen_planes_other0.0010.023644
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.7434.2317921
ELECTRON MICROSCOPYr_mcbond_other2.7424.2317921
ELECTRON MICROSCOPYr_mcangle_it5.0087.5839882
ELECTRON MICROSCOPYr_mcangle_other5.0097.5869883
ELECTRON MICROSCOPYr_scbond_it2.7675.0699119
ELECTRON MICROSCOPYr_scbond_other2.7675.0719120
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other5.1259.19213476
ELECTRON MICROSCOPYr_long_range_B_refined13.12157.1574992
ELECTRON MICROSCOPYr_long_range_B_other13.12157.1574993
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.604 14405 -
obs--100 %

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