8HMZ image
Deposition Date 2022-12-06
Release Date 2023-04-19
Last Version Date 2025-07-16
Entry Detail
PDB ID:
8HMZ
Keywords:
RNA BINDING PROTEIN/RNA
Title:
Cryo-EM structure of the human post-catalytic TSEN/pre-tRNA complex
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8HMZ validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:Pre-tRNA 3' END
Chain IDs:F (auth: 3)
Chain Length:42
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:Pre-tRNA 5' END
Chain IDs:E (auth: 5)
Chain Length:72
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:tRNA-splicing endonuclease subunit Sen2
Gene (Uniprot):TSEN2
Chain IDs:A
Chain Length:485
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8NCE0 Pfam ID:PF02778, PF01974 EC:4.6.1.16
Protein Blast
Polymer Type:polypeptide(L)
Molecule:tRNA-splicing endonuclease subunit Sen34
Gene (Uniprot):TSEN34
Chain IDs:B
Chain Length:330
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BSV6 Pfam ID:PF01974 EC:4.6.1.16
Protein Blast
Polymer Type:polypeptide(L)
Molecule:tRNA-splicing endonuclease subunit Sen54
Gene (Uniprot):TSEN54
Chain IDs:C
Chain Length:546
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z6J9 Pfam ID:PF12928 EC:4.6.1.16
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chromosome 1 open reading frame 19, isoform CRA_a
Chain IDs:D
Chain Length:213
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WW01 Pfam ID:PF09631
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polyribonucleotide 5'-hydroxyl-kinase Clp1
Gene (Uniprot):CLP1
Chain IDs:G (auth: E)
Chain Length:445
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92989 Pfam ID:PF16573, PF16575, PF06807 EC:2.7.1.78
Ligand Molecules
MG
Primary Citation
Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease.
Mol.Cell 83 1328 1339.e4 (2023)
PMID: 37028420 DOI: 10.1016/j.molcel.2023.03.015

Abstact

Removal of the intron from precursor-tRNA (pre-tRNA) is essential in all three kingdoms of life. In humans, this process is mediated by the tRNA splicing endonuclease (TSEN) comprising four subunits: TSEN2, TSEN15, TSEN34, and TSEN54. Here, we report the cryo-EM structures of human TSEN bound to full-length pre-tRNA in the pre-catalytic and post-catalytic states at average resolutions of 2.94 and 2.88 Å, respectively. Human TSEN features an extended surface groove that holds the L-shaped pre-tRNA. The mature domain of pre-tRNA is recognized by conserved structural elements of TSEN34, TSEN54, and TSEN2. Such recognition orients the anticodon stem of pre-tRNA and places the 3'-splice site and 5'-splice site into the catalytic centers of TSEN34 and TSEN2, respectively. The bulk of the intron sequences makes no direct interaction with TSEN, explaining why pre-tRNAs of varying introns can be accommodated and cleaved. Our structures reveal the molecular ruler mechanism of pre-tRNA cleavage by TSEN.

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Primary Citation of related structures
8HMZ