7ZRZ

Structure of the human tRNA splicing endonuclease defines substrate recognition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN.

Sekulovski, S.Susac, L.Stelzl, L.S.Tampe, R.Trowitzsch, S.

(2023) Nat Struct Mol Biol 30: 834-840

  • DOI: https://doi.org/10.1038/s41594-023-00992-y
  • Primary Citation of Related Structures:  
    7ZRZ

  • PubMed Abstract: 

    Heterotetrameric human transfer RNA (tRNA) splicing endonuclease TSEN catalyzes intron excision from precursor tRNAs (pre-tRNAs), utilizing two composite active sites. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH). Despite the essential function of TSEN, the three-dimensional assembly of TSEN-CLP1, the mechanism of substrate recognition, and the structural consequences of disease mutations are not understood in molecular detail. Here, we present single-particle cryogenic electron microscopy reconstructions of human TSEN with intron-containing pre-tRNAs. TSEN recognizes the body of pre-tRNAs and pre-positions the 3' splice site for cleavage by an intricate protein-RNA interaction network. TSEN subunits exhibit large unstructured regions flexibly tethering CLP1. Disease mutations localize far from the substrate-binding interface and destabilize TSEN. Our work delineates molecular principles of pre-tRNA recognition and cleavage by human TSEN and rationalizes mutations associated with PCH.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen34A [auth AP1]263Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen2B [auth BP4]260Homo sapiensMutation(s): 0 
Gene Names: TSEN2SEN2
EC: 4.6.1.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCE0 (Homo sapiens)
Explore Q8NCE0 
Go to UniProtKB:  Q8NCE0
PHAROS:  Q8NCE0
GTEx:  ENSG00000154743 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NCE0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen54C [auth CP1]293Homo sapiensMutation(s): 0 
Gene Names: TSEN54SEN54
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6J9 (Homo sapiens)
Explore Q7Z6J9 
Go to UniProtKB:  Q7Z6J9
PHAROS:  Q7Z6J9
GTEx:  ENSG00000182173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6J9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen15D [auth DP1]217Homo 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
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
pre-tRNA Arg TCT 3-2E [auth ZN1]89Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyTR 1711/1-7
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2023-06-07
    Changes: Database references
  • Version 1.3: 2023-06-28
    Changes: Database references