eF-site ID 6dbi-ABCDEFGHIJ PDB Code 6dbi Chain A, B, C, D, E, F, G, H, I, J click to enlarge Title Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates Classification RECOMBINATION/DNA Compound Recombination activating gene 1 - MBP chimera Source (6DBI) Sequence A:  GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVK SVCLTLFLLALRAGNEHKQADELEAMMQGRGFGLHPAVCL AIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRNAEK ELLPGFHQFEWQPALKNVSTSWDVGIIDGLSGWTVSVDDV PADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMC TSGFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTIM SISIRLEGEDDGITIFQEQKPNSELSCRPLCLMFVDESDH ETLTAILGPVVAERKAMMESRLIISVGGLLRSFRFFFRGT GYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNMVLHS ITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFM ETQPTLDALHCDIGNATEFYKIFQDEIGEVYQKPNPSREE RRRWRSTLDKQLRKKMKLKPVMRMNGNYARRLMTREAVEA VCELVPSEERREALLKLMDLYLQMKPVWRSTCPSRDCPDQ LCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLAHVPE IVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELE DILKHHWLYTSKYLQKFMEAHK B:  MSLQPLTAVNCGSLVQPGFSLLDLEGDVYLFGQKGWPKRS CPTGIFGVRIKKGELKLRAISFSNNSSYLPPLRCPAIAHF EAQDGKPECYLIHGGRTPNNELSSSLYMLSVDSRGCNRKV TLRCEEKELVGDVPSARYGHTLSVINSRGKTACVLFGGRS YMPPTERTTQNWNSVVDCPPQVYLIDLEFGCCTAHTLPEL TDGQSFHVALARQDCVYFLGGHILSSDCRPSRLIRLHVEL LLGSPVLTCTILHEGLTITSAIASPIGYHEYIIFGGYQSE TQKRMECTYVGLDDVGVHMESREPPQWTSEISHSRTWFGG SLGKGTALVAIPSEGNPTPPEAYHFYQVSFQ C:  GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVK SVCLTLFLLALRAGNEHKQADELEAMMQGRGFGLHPAVCL AIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRNAEK ELLPGFHQFEWQPALKNVSTSWDVGIIDGLSGWTVSVDDV PADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMC TSGFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTIM SISIRLEGEDDGITIFQEQKPNSELSCRPLCLMFVDESDH ETLTAILGPVVAERKAMMESRLIISVGGLLRSFRFFFRGT GYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNMVLHS ITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFM ETQPTLDALHCDIGNATEFYKIFQDEIGEVYQKPNPSREE RRRWRSTLDKQLRKKMKLKPVMRMNGNYARRLMTREAVEA VCELVPSEERREALLKLMDLYLQMKPVWRSTCPSRDCPDQ LCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLAHVPE IVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELE DILKHHWLYTSKYLQKFMEAHK D:  MSLQPLTAVNCGSLVQPGFSLLDLEGDVYLFGQKGWPKRS CPTGIFGVRIKKGELKLRAISFSNNSSYLPPLRCPAIAHF EAQDGKPECYLIHGGRTPNNELSSSLYMLSVDSRGCNRKV TLRCEEKELVGDVPSARYGHTLSVINSRGKTACVLFGGRS YMPPTERTTQNWNSVVDCPPQVYLIDLEFGCCTAHTLPEL TDGQSFHVALARQDCVYFLGGHILSSDCRPSRLIRLHVEL LLGSPVLTCTILHEGLTITSAIASPIGYHEYIIFGGYQSE TQKRMECTYVGLDDVGVHMESREPPQWTSEISHSRTWFGG SLGKGTALVAIPSEGNPTPPEAYHFYQVSFQ E:  CACAGTGCTACAGACTGGAACAAAAACCCTGCAG F:  CTGCAGGGTTTTTGTTCCAGTCTGTAGCACTGTGTAAGAC AGGCCAGATC G:  CTGCAGGGTTTTTGTACAGCCAGACAGTGGAGTACTACCA CTGTGTAAGACAGGCCAGATC H:  CACAGTGGTAGTACTCCACTGTCTGGCTGTACAAAAACCC TGCAG I:  GATCTGGCCTGTCTTA J:  GATCTGGCCTGTCTTA Description Functional site 1) chain C residue 749 type sequence C description binding site for residue ZN C 1101 source : AC1 2) chain C residue 752 type sequence C description binding site for residue ZN C 1101 source : AC1 3) chain C residue 959 type sequence H description binding site for residue ZN C 1101 source : AC1 4) chain C residue 964 type sequence H description binding site for residue ZN C 1101 source : AC1 5) chain C residue 684 type sequence E description binding site for residue CA C 1102 source : AC2 6) chain C residue 730 type sequence D description binding site for residue CA C 1102 source : AC2 7) chain G residue 46 type sequence T description binding site for residue CA C 1102 source : AC2 8) chain J residue 16 type sequence A description binding site for residue CA C 1102 source : AC2 9) chain C residue 620 type sequence D description binding site for residue CA C 1103 source : AC3 10) chain C residue 621 type sequence G description binding site for residue CA C 1103 source : AC3 11) chain G residue 45 type sequence G description binding site for residue CA C 1103 source : AC3 12) chain G residue 46 type sequence T description binding site for residue CA C 1103 source : AC3 13) chain A residue 749 type sequence C description binding site for residue ZN A 1101 source : AC4 14) chain A residue 752 type sequence C description binding site for residue ZN A 1101 source : AC4 15) chain A residue 959 type sequence H description binding site for residue ZN A 1101 source : AC4 16) chain A residue 964 type sequence H description binding site for residue ZN A 1101 source : AC4 17) chain A residue 684 type sequence E description binding site for residue CA A 1102 source : AC5 18) chain I residue 16 type sequence A description binding site for residue CA A 1102 source : AC5 19) chain A residue 620 type sequence D description binding site for residue CA A 1103 source : AC6 20) chain A residue 730 type sequence D description binding site for residue CA A 1103 source : AC6 21) chain F residue 35 type sequence T description binding site for residue CA A 1103 source : AC6 22) chain I residue 16 type sequence A description binding site for residue CA A 1103 source : AC6 23) chain C residue 408-475 type DNA_BIND sequence GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVK SVCLTLFLLALRAGNEHKQADELEAMMQ description NBD => ECO:0000255|PROSITE-ProRule:PRU00820 source Swiss-Prot : SWS_FT_FI3 24) chain A residue 408-475 type DNA_BIND sequence GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVK SVCLTLFLLALRAGNEHKQADELEAMMQ description NBD => ECO:0000255|PROSITE-ProRule:PRU00820 source Swiss-Prot : SWS_FT_FI3 25) chain C residue 620 type BINDING sequence D description BINDING => ECO:0000250 source Swiss-Prot : SWS_FT_FI4 26) chain C residue 730 type BINDING sequence D description BINDING => ECO:0000250 source Swiss-Prot : SWS_FT_FI4 27) chain C residue 984 type BINDING sequence E description BINDING => ECO:0000250 source Swiss-Prot : SWS_FT_FI4 28) chain A residue 620 type BINDING sequence D description BINDING => ECO:0000250 source Swiss-Prot : SWS_FT_FI4 29) chain A residue 730 type BINDING sequence D description BINDING => ECO:0000250 source Swiss-Prot : SWS_FT_FI4 30) chain A residue 984 type BINDING sequence E description BINDING => ECO:0000250 source Swiss-Prot : SWS_FT_FI4 31) chain C residue 915 type SITE sequence W description Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage site => ECO:0000250 source Swiss-Prot : SWS_FT_FI6 32) chain A residue 915 type SITE sequence W description Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage site => ECO:0000250 source Swiss-Prot : SWS_FT_FI6

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