8CBL

Structure of human mitochondrial RNase Z in complex with mitochondrial pre-tRNA-His(0,Ser)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for human mitochondrial tRNA maturation.

Meynier, V.Hardwick, S.W.Catala, M.Roske, J.J.Oerum, S.Chirgadze, D.Y.Barraud, P.Yue, W.W.Luisi, B.F.Tisne, C.

(2024) Nat Commun 15: 4683-4683

  • DOI: https://doi.org/10.1038/s41467-024-49132-0
  • Primary Citation of Related Structures:  
    8CBK, 8CBL, 8CBM, 8CBO

  • PubMed Abstract: 

    The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by the mitochondrial endoribonucleases (mt-RNase), P and Z, releases all RNA species from the two RNA transcripts. The tRNAs then undergo 3'-CCA addition. In metazoan mitochondria, RNase P is a multi-enzyme assembly that comprises the endoribonuclease PRORP and a tRNA methyltransferase subcomplex. The requirement for this tRNA methyltransferase subcomplex for mt-RNase P cleavage activity, as well as the mechanisms of pre-tRNA 3'-cleavage and 3'-CCA addition, are still poorly understood. Here, we report cryo-EM structures that visualise four steps of mitochondrial tRNA maturation: 5' and 3' tRNA-end processing, methylation and 3'-CCA addition, and explain the defined sequential order of the tRNA processing steps. The methyltransferase subcomplex recognises the pre-tRNA in a distinct mode that can support tRNA-end processing and 3'-CCA addition, likely resulting from an evolutionary adaptation of mitochondrial tRNA maturation complexes to the structurally-fragile mitochondrial tRNAs. This subcomplex can also ensure a tRNA-folding quality-control checkpoint before the sequential docking of the maturation enzymes. Altogether, our study provides detailed molecular insight into RNA-transcript processing and tRNA maturation in human mitochondria.


  • Organizational Affiliation

    Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyacyl-CoA dehydrogenase type-2
A, B, C, D
261Homo sapiensMutation(s): 0 
Gene Names: HSD17B10ERABHADH2MRPP2SCHADSDR5C1XH98G2
EC: 1.1.1.35 (PDB Primary Data), 1.1.1.62 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.178 (PDB Primary Data), 1.1.1.53 (PDB Primary Data), 1.1.1.159 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99714 (Homo sapiens)
Explore Q99714 
Go to UniProtKB:  Q99714
PHAROS:  Q99714
GTEx:  ENSG00000072506 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99714
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc phosphodiesterase ELAC protein 2826Homo sapiensMutation(s): 1 
Gene Names: ELAC2HPC2
EC: 3.1.26.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ52 (Homo sapiens)
Explore Q9BQ52 
Go to UniProtKB:  Q9BQ52
PHAROS:  Q9BQ52
GTEx:  ENSG00000006744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQ52
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA methyltransferase 10 homolog C408Homo sapiensMutation(s): 0 
Gene Names: TRMT10CMRPP1RG9MTD1
EC: 2.1.1 (PDB Primary Data), 2.1.1.218 (PDB Primary Data), 2.1.1.221 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L0Y3 (Homo sapiens)
Explore Q7L0Y3 
Go to UniProtKB:  Q7L0Y3
PHAROS:  Q7L0Y3
GTEx:  ENSG00000174173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L0Y3
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
Mitochondrial Precursor tRNA-His(0,Ser)G [auth T]128Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.8.9.1
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-19-CE07-0028

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release