9LZT
RfxCas13d-crRNA binary complex
Summary for 9LZT
| Entry DOI | 10.2210/pdb9lzt/pdb |
| EMDB information | 63530 |
| Descriptor | RNA (51-MER), RfxCas13d, MAGNESIUM ION (3 entities in total) |
| Functional Keywords | cas13d, rna, complex, rna binding protein/rna, rna binding protein-rna complex |
| Biological source | Ruminococcus sp. XPD3002 More |
| Total number of polymer chains | 2 |
| Total formula weight | 127859.04 |
| Authors | Yang, Q.X.,Sun, Y.F. (deposition date: 2025-02-22, release date: 2025-10-08, Last modification date: 2026-03-11) |
| Primary citation | Yang, Q.,Sun, Y.,Sun, L.,Chi, T.,Chen, Z. Cryo-EM structure of the RfxCas13d-crRNA-off-target-RNA complex. Structure, 34:11-19.e2, 2026 Cited by PubMed Abstract: The CRISPR-Cas system is crucial for the adaptive immune response of prokaryotes and has been widely applied for genetic engineering. Cas13d, a type VI-D CRISPR-Cas effector, functions as RNA-guided ribonuclease and has been engineered for programmable RNA editing, which is a commonly used, active, and well-characterized small type VI editor. Here, we determined cryoelectron microscopy (cryo-EM) structures of Ruminococcus flavefaciens Cas13d in a RfxCas13d-crRNA-off-target-RNA ternary complex and RfxCas13d-crRNA binary complex at 3.10 and 3.13 Å resolution. The ternary complex consists of RfxCas13d, crRNA, and a captured short off-target ssRNA at a complex state of binding proximal mismatched RNA. RfxCas13d undergoes conformational changes with or without the off-target RNA, but the catalytic sites remain unchanged. Mg aids in stabilizing the crRNA repeat region structure, which may be crucial for RNA binding. This discovery provides the foundation for developing RfxCas13d as a mature tool and offers a framework for advancing transcriptome engineering. PubMed: 41135510DOI: 10.1016/j.str.2025.09.010 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.1 Å) |
Structure validation
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