9YYG
AI-generated RNA-guided nuclease TAM-bound state
Summary for 9YYG
| Entry DOI | 10.2210/pdb9yyg/pdb |
| EMDB information | 73644 |
| Descriptor | AI-designed RNA-guided nuclease, RNA (116-MER), DNA (5'-D(*GP*GP*TP*TP*GP*AP*TP*C)-3'), ... (4 entities in total) |
| Functional Keywords | crispr, nuclease, ai, evolution scale modeling, inverse folding, esm-if1, tnpb, tam, pam, spacer, exonuclease, dna binding protein-dna complex, enzyme, ribonucleoprotein, rna, rna-guided nuclease, cas12, isdra2, esm, rna binding protein |
| Biological source | synthetic construct More |
| Total number of polymer chains | 4 |
| Total formula weight | 94403.49 |
| Authors | Skopintsev, P.,Esain-Garcia, I.,Doudna, J. (deposition date: 2025-10-29, release date: 2026-07-15, Last modification date: 2026-07-29) |
| Primary citation | Skopintsev, P.,Esain-Garcia, I.,DeTurk, E.C.,Yoon, P.H.,Zhou, Z.,Weiss, T.,Kamalu, M.,Chamraj, A.,Loi, K.J.,Langeberg, C.J.,Boger, R.S.,Nisonoff, H.,Karp, H.M.,Chen, L.X.,Shi, H.,Vohra, K.,Banfield, J.F.,Cate, J.H.D.,Jacobsen, S.E.,Doudna, J.A. Structure and evolution-guided design of minimal RNA-guided nucleases. Science, 393:313-318, 2026 Cited by PubMed Abstract: The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic properties remains challenging. Here, we use a protein design strategy that couples a structure-guided inverse-folding model with evolution-informed residue constraints to generate active, divergent variants of TnpB, a minimal CRISPR-Cas12-like nuclease, termed SynTnpBs. High-throughput screening of artificial intelligence-generated variants yielded editors that retained or exceeded wild-type activity in bacterial, plant, and human cells. Cryo-electron microscopy-based structure determination of the most divergent variant revealed stabilizing contacts in the RNA-DNA interfaces across conformations, demonstrating the design potential of this approach. Together, these results establish a strategy for creating non-natural RNA-guided nucleases and conformationally active nucleic acid binders, enlarging the designable protein space. PubMed: 42462008DOI: 10.1126/science.aed6123 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.8 Å) |
Structure validation
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