Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures

Cell. 2015 Nov 19;163(5):1138-1152. doi: 10.1016/j.cell.2015.10.055. Epub 2015 Nov 5.


Diverse repertoires of antigen-receptor genes that result from combinatorial splicing of coding segments by V(D)J recombination are hallmarks of vertebrate immunity. The (RAG1-RAG2)2 recombinase (RAG) recognizes recombination signal sequences (RSSs) containing a heptamer, a spacer of 12 or 23 base pairs, and a nonamer (12-RSS or 23-RSS) and introduces precise breaks at RSS-coding segment junctions. RAG forms synaptic complexes only with one 12-RSS and one 23-RSS, a dogma known as the 12/23 rule that governs the recombination fidelity. We report cryo-electron microscopy structures of synaptic RAG complexes at up to 3.4 Å resolution, which reveal a closed conformation with base flipping and base-specific recognition of RSSs. Distortion at RSS-coding segment junctions and base flipping in coding segments uncover the two-metal-ion catalytic mechanism. Induced asymmetry involving tilting of the nonamer-binding domain dimer of RAG1 upon binding of HMGB1-bent 12-RSS or 23-RSS underlies the molecular mechanism for the 12/23 rule.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cryoelectron Microscopy
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / ultrastructure
  • Homeodomain Proteins / chemistry*
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / ultrastructure
  • Humans
  • Mice
  • Molecular Sequence Data
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / ultrastructure
  • Mutation
  • Sequence Alignment
  • V(D)J Recombination*
  • Zebrafish


  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Multiprotein Complexes
  • V(D)J recombination activating protein 2
  • RAG-1 protein