6Z9U

Crystal structure of a TSEN15-34 heterodimer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia.

Sekulovski, S.Devant, P.Panizza, S.Gogakos, T.Pitiriciu, A.Heitmeier, K.Ramsay, E.P.Barth, M.Schmidt, C.Tuschl, T.Baas, F.Weitzer, S.Martinez, J.Trowitzsch, S.

(2021) Nat Commun 12: 5610-5610

  • DOI: https://doi.org/10.1038/s41467-021-25870-3
  • Primary Citation of Related Structures:  
    6Z9U

  • PubMed Abstract: 

    Introns of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15-34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes.


  • Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen34
A, C
104Homo sapiensMutation(s): 0 
Gene Names: TSEN34LENG5SEN34
EC: 4.6.1.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSV6 (Homo sapiens)
Explore Q9BSV6 
Go to UniProtKB:  Q9BSV6
PHAROS:  Q9BSV6
GTEx:  ENSG00000170892 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSV6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen15
B, D
167Homo sapiensMutation(s): 0 
Gene Names: TSEN15C1orf19SEN15
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WW01 (Homo sapiens)
Explore Q8WW01 
Go to UniProtKB:  Q8WW01
PHAROS:  Q8WW01
GTEx:  ENSG00000198860 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WW01
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.848α = 90
b = 69.277β = 98.308
c = 94.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyTR 1711/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description