8ISS

Cryo-EM structure of wild-type human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG at 3.19 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Recognition and cleavage mechanism of intron-containing pre-tRNA by human TSEN endonuclease complex.

Yuan, L.Han, Y.Zhao, J.Zhang, Y.Sun, Y.

(2023) Nat Commun 14: 6071-6071

  • DOI: https://doi.org/10.1038/s41467-023-41845-y
  • Primary Citation of Related Structures:  
    8ISS

  • PubMed Abstract: 

    Removal of introns from transfer RNA precursors (pre-tRNAs) occurs in all living organisms. This is a vital phase in the maturation and functionality of tRNA. Here we present a 3.2 Å-resolution cryo-EM structure of an active human tRNA splicing endonuclease complex bound to an intron-containing pre-tRNA. TSEN54, along with the unique regions of TSEN34 and TSEN2, cooperatively recognizes the mature body of pre-tRNA and guides the anticodon-intron stem to the correct position for splicing. We capture the moment when the endonucleases are poised for cleavage, illuminating the molecular mechanism for both 3' and 5' cleavage reactions. Two insertion loops from TSEN54 and TSEN2 cover the 3' and 5' splice sites, respectively, trapping the scissile phosphate in the center of the catalytic triad of residues. Our findings reveal the molecular mechanism for eukaryotic pre-tRNA recognition and cleavage, as well as the evolutionary relationship between archaeal and eukaryotic TSENs.


  • Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, Shanghai, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen15180Homo 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 
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UniProt GroupQ8WW01
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen2465Homo 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 
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UniProt GroupQ8NCE0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen34310Homo 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 
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UniProt GroupQ9BSV6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease subunit Sen54530Homo 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 
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UniProt GroupQ7Z6J9
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (88-MER)88Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2023-10-18
    Type: Initial release