6DBQ
Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs
Summary for 6DBQ
| Entry DOI | 10.2210/pdb6dbq/pdb |
| Related | 6DBI 6DBJ 6DBL 6DBO 6DBQ 6DBR 6DBU 6DBV 6DBW 6DBX |
| EMDB information | 7843 7844 7845 7846 7847 7848 7849 7850 7851 7852 7853 |
| Descriptor | Recombination activating gene 1 - MBP chimera, Recombination activating gene 2, Molecule name: Forward strand of 12-RSS substrate DNA, ... (8 entities in total) |
| Functional Keywords | v(d)j recombination, rag complex, rss substrate dna, pre-cleveaage complex, recombination-dna complex, recombination/dna |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 8 |
| Total formula weight | 449889.93 |
| Authors | |
| Primary citation | Ru, H.,Mi, W.,Zhang, P.,Alt, F.W.,Schatz, D.G.,Liao, M.,Wu, H. DNA melting initiates the RAG catalytic pathway. Nat. Struct. Mol. Biol., 25:732-742, 2018 Cited by PubMed Abstract: The mechanism for initiating DNA cleavage by DDE-family enzymes, including the RAG endonuclease, which initiates V(D)J recombination, is not well understood. Here we report six cryo-EM structures of zebrafish RAG in complex with one or two intact recombination signal sequences (RSSs), at up to 3.9-Å resolution. Unexpectedly, these structures reveal DNA melting at the heptamer of the RSSs, thus resulting in a corkscrew-like rotation of coding-flank DNA and the positioning of the scissile phosphate in the active site. Substrate binding is associated with dimer opening and a piston-like movement in RAG1, first outward to accommodate unmelted DNA and then inward to wedge melted DNA. These precleavage complexes show limited base-specific contacts of RAG at the conserved terminal CAC/GTG sequence of the heptamer, thus suggesting conservation based on a propensity to unwind. CA and TG overwhelmingly dominate terminal sequences in transposons and retrotransposons, thereby implicating a universal mechanism for DNA melting during the initiation of retroviral integration and DNA transposition. PubMed: 30061602DOI: 10.1038/s41594-018-0098-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (4.22 Å) |
Structure validation
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