eF-site ID 6dbi-ABCD
PDB Code 6dbi
Chain A, B, C, D

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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
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 C
residue 620
type
sequence D
description binding site for residue CA C 1103
source : AC3

8) chain C
residue 621
type
sequence G
description binding site for residue CA C 1103
source : AC3

9) chain A
residue 749
type
sequence C
description binding site for residue ZN A 1101
source : AC4

10) chain A
residue 752
type
sequence C
description binding site for residue ZN A 1101
source : AC4

11) chain A
residue 959
type
sequence H
description binding site for residue ZN A 1101
source : AC4

12) chain A
residue 964
type
sequence H
description binding site for residue ZN A 1101
source : AC4

13) chain A
residue 684
type
sequence E
description binding site for residue CA A 1102
source : AC5

14) chain A
residue 620
type
sequence D
description binding site for residue CA A 1103
source : AC6

15) chain A
residue 730
type
sequence D
description binding site for residue CA A 1103
source : AC6

16) chain C
residue 408-475
type DNA_BIND
sequence GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVK
SVCLTLFLLALRAGNEHKQADELEAMMQ
description NBD => ECO:0000255|PROSITE-ProRule:PRU00820
source Swiss-Prot : SWS_FT_FI3

17) chain A
residue 408-475
type DNA_BIND
sequence GGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVK
SVCLTLFLLALRAGNEHKQADELEAMMQ
description NBD => ECO:0000255|PROSITE-ProRule:PRU00820
source Swiss-Prot : SWS_FT_FI3

18) chain C
residue 620
type BINDING
sequence D
description BINDING => ECO:0000250
source Swiss-Prot : SWS_FT_FI4

19) chain C
residue 730
type BINDING
sequence D
description BINDING => ECO:0000250
source Swiss-Prot : SWS_FT_FI4

20) chain C
residue 984
type BINDING
sequence E
description BINDING => ECO:0000250
source Swiss-Prot : SWS_FT_FI4

21) chain A
residue 620
type BINDING
sequence D
description BINDING => ECO:0000250
source Swiss-Prot : SWS_FT_FI4

22) chain A
residue 730
type BINDING
sequence D
description BINDING => ECO:0000250
source Swiss-Prot : SWS_FT_FI4

23) chain A
residue 984
type BINDING
sequence E
description BINDING => ECO:0000250
source Swiss-Prot : SWS_FT_FI4

24) 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

25) 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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