8RR3

Human mitochondrial RNase Z complex with ELAC2-D550N catalytic mutant and tRNA-Gln precursor (Composite model)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Molecular basis of human nuclear and mitochondrial tRNA 3' processing.

Bhatta, A.Kuhle, B.Yu, R.D.Spanaus, L.Ditter, K.Bohnsack, K.E.Hillen, H.S.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01445-w
  • Primary Citation of Related Structures:  
    8RR3, 8RR4

  • PubMed Abstract: 

    Eukaryotic transfer RNA (tRNA) precursors undergo sequential processing steps to become mature tRNAs. In humans, ELAC2 carries out 3' end processing of both nucleus-encoded (nu-tRNAs) and mitochondria-encoded (mt-tRNAs) tRNAs. ELAC2 is self-sufficient for processing of nu-tRNAs but requires TRMT10C and SDR5C1 to process most mt-tRNAs. Here we show that TRMT10C and SDR5C1 specifically facilitate processing of structurally degenerate mt-tRNAs lacking the canonical elbow. Structures of ELAC2 in complex with TRMT10C, SDR5C1 and two divergent mt-tRNA substrates reveal two distinct mechanisms of pre-tRNA recognition. While canonical nu-tRNAs and mt-tRNAs are recognized by direct ELAC2-RNA interactions, processing of noncanonical mt-tRNAs depends on protein-protein interactions between ELAC2 and TRMT10C. These results provide the molecular basis for tRNA 3' processing in both the nucleus and the mitochondria and explain the organelle-specific requirement for additional factors. Moreover, they suggest that TRMT10C-SDR5C1 evolved as a mitochondrial tRNA maturation platform to compensate for the structural erosion of mt-tRNAs in bilaterian animals.


  • Organizational Affiliation

    Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.


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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc phosphodiesterase ELAC protein 2798Homo 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA methyltransferase 10 homolog C315Homo 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
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Human mitochondrial tRNA-Gln precursor with 3' trailer RNAG [auth T]96Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1190
German Research Foundation (DFG)GermanyFOR2848
German Research Foundation (DFG)GermanySFB1565
German Research Foundation (DFG)GermanyEXC 2067/1 390729940
European Research Council (ERC)European Union101116869

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references