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- PDB-8z1f: Cryo-EM structure of human ELAC2-tRNA -

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Basic information

Entry
Database: PDB / ID: 8z1f
TitleCryo-EM structure of human ELAC2-tRNA
Components
  • Homo sapiens mitochondrion pre-tRNA-Tyr
  • Zinc phosphodiesterase ELAC protein 2
KeywordsRNA BINDING PROTEIN / endonuclease Zinc phosphodiesterase
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
PHOSPHATE ION / : / RNA / RNA (> 10) / Zinc phosphodiesterase ELAC protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLiu, Z.M. / Xue, C.Y.
Funding support1items
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 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: Homo sapiens mitochondrion pre-tRNA-Tyr
A: Zinc phosphodiesterase ELAC protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2965
Polymers120,0712
Non-polymers2263
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain Homo sapiens mitochondrion pre-tRNA-Tyr


Mass: 27722.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1851980260
#2: 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: 92348.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELAC2, HPC2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9BQ52, tRNase Z
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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
1ELAC2-tRNACOMPLEX#1-#20MULTIPLE SOURCES
2tRNACOMPLEX#11SYNTHETIC
3ELAC2 proteinCOMPLEX#21RECOMBINANT
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34974 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026916
ELECTRON MICROSCOPYf_angle_d0.4869695
ELECTRON MICROSCOPYf_dihedral_angle_d17.7281646
ELECTRON MICROSCOPYf_chiral_restr0.0441148
ELECTRON MICROSCOPYf_plane_restr0.0031002

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