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- EMDB-39710: Cryo-EM structure of human ELAC2 -

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Basic information

Entry
Database: EMDB / ID: EMD-39710
TitleCryo-EM structure of human ELAC2
Map dataELAC2
Sample
  • Complex: ELAC2 protein
    • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
  • Ligand: ZINC ION
  • Ligand: PHOSPHATE ION
Keywordsendonuclease Zinc phosphodiesterase / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNase Z / mitochondrial tRNA processing / rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / 3'-tRNA processing endoribonuclease activity / tRNA 3'-end processing / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay ...tRNase Z / mitochondrial tRNA processing / rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / 3'-tRNA processing endoribonuclease activity / tRNA 3'-end processing / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / tRNA processing in the nucleus / mitochondrial nucleoid / RNA endonuclease activity / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
tRNase Z endonuclease / : / tRNase Z endonuclease / Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Zinc phosphodiesterase ELAC protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu ZM / Xue CY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural insights into human ELAC2 as a tRNA 3' processing enzyme.
Authors: Chenyang Xue / Junshan Tian / Yanhong Chen / Zhongmin Liu /
Abstract: Human elaC ribonuclease Z 2 (ELAC2) removes the 3' trailer of precursor transfer ribonucleic acid (pre-tRNA). Mutations in ELAC2 are highly associated with the development of prostate cancer and ...Human elaC ribonuclease Z 2 (ELAC2) removes the 3' trailer of precursor transfer ribonucleic acid (pre-tRNA). Mutations in ELAC2 are highly associated with the development of prostate cancer and hypertrophic cardiomyopathy. However, the catalytic mechanism of ELAC2 remains unclear. We determined the cryogenic electron microscopy structures of human ELAC2 in various states, including the apo, pre-tRNA-bound and tRNA-bound states, which enabled us to identify the structural basis for its binding to pre-tRNA and cleavage of the 3' trailer. Notably, conformational rearrangement of the C-terminal helix was related to feeding of the 3' trailer into the cleavage site, possibly explaining why its mutations are associated with disease. We further used biochemical assays to analyse the structural effects of disease-related mutations of human ELAC2. Collectively, our data provide a comprehensive structural basis for how ELAC2 recruits pre-tRNA via its flexible arm domain and guides the 3' trailer of pre-tRNA into the active centre for cleavage by its C-terminal helix.
History
DepositionApr 10, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39710.png

Downloads & links

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Map

FileDownload / File: emd_39710.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationELAC2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 300 pix.
= 157.8 Å		0.53 Å/pix.
x 300 pix.
= 157.8 Å		0.53 Å/pix.
x 300 pix.
= 157.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.526 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0574
Minimum - Maximum-0.39800924 - 0.63860154
Average (Standard dev.)-0.0005191498 (±0.020396283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 157.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: E2-halfA

Fileemd_39710_half_map_1.map
AnnotationE2-halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: E2-halfB

Fileemd_39710_half_map_2.map
AnnotationE2-halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ELAC2 protein

EntireName: ELAC2 protein
Components
  • Complex: ELAC2 protein
    • Protein or peptide: Zinc phosphodiesterase ELAC protein 2
  • Ligand: ZINC ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: ELAC2 protein

SupramoleculeName: ELAC2 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F

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Macromolecule #1: Zinc phosphodiesterase ELAC protein 2

MacromoleculeName: Zinc phosphodiesterase ELAC protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNase Z
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.348117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 SHLHADHHTG 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 #2: ZINC ION

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

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243825
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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