8KGF

Structure of AmCas12a with crRNA

Summary for 8KGF

• Entry DOI: 10.2210/pdb8kgf/pdb
• EMDB information: 37219
• Descriptor: CRISPR-associated endonuclease Cas12a, RNA (44-MER), MAGNESIUM ION (3 entities in total)
• Functional Keywords: crispr/cas12a, dna binding protein, dna binding protein-rna complex, dna binding protein/rna
• Biological source: Anaeroglobus; More
• Total number of polymer chains: 2
• Total formula weight: 171486.37

Authors

Feng, Y.,Zhang, X.,Shi, J.,Ma, P.,Tang, J.,Huang, X. (deposition date: 2023-08-18, release date: 2024-09-04, Last modification date: 2025-09-24)

Primary citation

Feng, Y.,Shi, J.,Li, Z.,Li, Y.,Yang, J.,Huang, S.,Zheng, J.,Han, W.,Qiao, Y.,Zhang, J.,Liu, Q.,Yang, Y.,Hu, C.,Wu, L.,Zhang, X.,Tang, J.,Huang, X.,Ma, P.
Discovery of CRISPR-Cas12a clades using a large language model.
Nat Commun, 16:7877-7877, 2025

PubMed Abstract: CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments. In this work, we employ an evolutionary scale language model (ESM) to learn the information beyond sequences. Trained with CRISPR-Cas data, ESM accurately identifies Cas proteins without alignment. Limited experimental data restricts feature prediction, but integrating with machine learning enables trans-cleavage activity prediction of uncharacterized Cas12a. We discover 7 undocumented Cas12a subtypes with unique CRISPR loci. Structural analyses reveal 8 subtypes of Cas1, Cas2, and Cas4. Cas12a subtypes display distinct 3D-folds. CryoEM analyses unveil unique RNA interactions with the uncharacterized Cas12a. These proteins show distinct double-strand and single-strand DNA cleavage preferences and broad PAM recognition. Finally, we establish a specific detection strategy for the oncogene SNP without traditional Cas12a PAM. This study highlights the potential of language models in exploring undocumented Cas protein function via gene cluster classification.

PubMed: 40849498
DOI: 10.1038/s41467-025-63160-4

Experimental method

ELECTRON MICROSCOPY (2.9 Å)