7UXA

Human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG

  • Classification: SPLICING/RNA
  • Organism(s): Homo sapiens, synthetic construct
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2022-05-05 Released: 2023-02-08 
  • Deposition Author(s): Stanley, R.E., Hayne, C.K.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 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 for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex.

Hayne, C.K.Butay, K.J.U.Stewart, Z.D.Krahn, J.M.Perera, L.Williams, J.G.Petrovitch, R.M.Deterding, L.J.Matera, A.G.Borgnia, M.J.Stanley, R.E.

(2023) Nat Struct Mol Biol 30: 824-833

  • DOI: https://doi.org/10.1038/s41594-023-00991-z
  • Primary Citation of Related Structures:  
    7UXA

  • PubMed Abstract: 

    Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is initiated by the heterotetrameric tRNA splicing endonuclease (TSEN) complex. All TSEN subunits are essential, and mutations within the complex are associated with a family of neurodevelopmental disorders known as pontocerebellar hypoplasia (PCH). Here, we report cryo-electron microscopy structures of the human TSEN-pre-tRNA complex. These structures reveal the overall architecture of the complex and the extensive tRNA binding interfaces. The structures share homology with archaeal TSENs but contain additional features important for pre-tRNA recognition. The TSEN54 subunit functions as a pivotal scaffold for the pre-tRNA and the two endonuclease subunits. Finally, the TSEN structures enable visualization of the molecular environments of PCH-causing missense mutations, providing insight into the mechanism of pre-tRNA splicing and PCH.


  • Organizational Affiliation

    Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA. chayne@uchicago.edu.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen34352Homo sapiensMutation(s): 3 
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen15183Homo 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen2483Homo sapiensMutation(s): 3 
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
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen54551Homo 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
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (78-MER)88synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA ES103247
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIC ES102488
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIC ES103206
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIC ES102487
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZI ES043010
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIC ES103326
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1K99-GM143534
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM136435

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2023-06-07
    Changes: Database references
  • Version 1.3: 2023-07-05
    Changes: Database references