9EY2 | pdb_00009ey2

Human mitochondrial RNase Z with tRNA-His-CCA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex.

Valentin Gese, G., Hallberg, B.M.

(2024) EMBO J 43: 6573-6590

  • DOI: https://doi.org/10.1038/s44318-024-00297-w
  • Primary Citation of Related Structures:  
    9EY0, 9EY1, 9EY2, 9GCH

  • PubMed 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 mitochondrial RNase Z complex (ELAC2/SDR5C1/TRMT10C) bound to different maturation states of mitochondrial tRNA His , 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.

    • Organizational Affiliation: 

    Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden.


Macromolecules

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(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: HSD17B10, ERAB, HADH2, MRPP2, SCHAD, SDR5C1, XH98G2
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
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA methyltransferase 10 homolog CE [auth F]356Homo sapiensMutation(s): 0 
Gene Names: TRMT10C, MRPP1, RG9MTD1
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
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc phosphodiesterase ELAC protein 2G [auth E]797Homo sapiensMutation(s): 0 
Gene Names: ELAC2, HPC2
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Data collection, Database references