9I8V
Cryo-EM structure of the Danio rerio tRNA ligase complex
Summary for 9I8V
| Entry DOI | 10.2210/pdb9i8v/pdb |
| EMDB information | 50108 52744 |
| Descriptor | ATP-dependent RNA helicase, RNA-splicing ligase RtcB homolog, Family with sequence similarity 98, member B, ... (5 entities in total) |
| Functional Keywords | trna ligase complex, rtcb, trna, trna maturation, trna splicing, ligase, rna binding protein |
| Biological source | Danio rerio (zebrafish) More |
| Total number of polymer chains | 5 |
| Total formula weight | 133388.99 |
| Authors | Chamera, S.,Zajko, W.,Czarnocki-Cieciura, M.,Jaciuk, M.,Koziej, L.,Nowak, J.,Wycisk, K.,Sroka, M.,Chramiec-Glabik, A.,Smietanski, M.,Golebiowski, F.,Warminski, M.,Jemielity, J.,Glatt, S.,Nowotny, M. (deposition date: 2025-02-06, release date: 2025-04-23, Last modification date: 2025-05-21) |
| Primary citation | Chamera, S.,Zajko, W.,Czarnocki-Cieciura, M.,Jaciuk, M.,Koziej, L.,Nowak, J.,Wycisk, K.,Sroka, M.,Chramiec-Glabik, A.,Smietanski, M.,Golebiowski, F.,Warminski, M.,Jemielity, J.,Glatt, S.,Nowotny, M. Structural and biochemical characterization of the 3'-5' tRNA splicing ligases. J.Biol.Chem., 301:108506-108506, 2025 Cited by PubMed Abstract: In archaea and metazoa, tRNA exons are ligated by the RNA ligases RtcB and RTCB, respectively. The metazoan RTCB forms a stable complex with four additional subunits, DDX1, FAM98B, CGI99 and ASHWIN. The role and assembly of these four components remain elusive. Furthermore, we lack structural information of how RNA substrates are recognized by 3'-5' tRNA ligases. Here, we use thiol-based chemical cross-linking to confirm the involvement of specific residues of RtcB in RNA binding and we present a cryo-electron microscopy structure of the purified five-subunit D. rerio tRNA ligase complex. The structure implies that the DDX1 helicase module is mobile and can modulate the activity of RTCB. Taken together, the presented results enhance our mechanistic understanding of RNA binding by 3'-5' tRNA splicing ligases and architecture of the metazoan tRNA ligase complex. PubMed: 40220997DOI: 10.1016/j.jbc.2025.108506 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.33 Å) |
Structure validation
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