NDB ID: 6CIM PDB ID: 6CIM 
Title:
PRE-REACTION COMPLEX, RAG1(E962Q)/2-NICKED/INTACT 12/23RSS COMPLEX IN MN2+
Molecular Description:
V(D)J recombination-activating protein 1
V(D)J recombination-activating protein 2
High mobility group protein B1/DNA Complex
Deposited:
2018-02-24
Released:
2018-04-25
Structural Keywords:
RH DOUBLE HELIX
Nucleic Acid Sequence:
Click to show/hide 5 nucleic acid sequences
Chain I
(DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA)
Chain F
(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DA)(DG)(DG)(DG)(DC)(DT)(DG) (DT)(DA)(
DT)(DC)(DA)(DC)(DT)(DG)(DT)(DG)(DT)(DA)(DA)(DG)(DA)(DC)(DA)(DG)(DG)(DC)
Chain G
(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DT)(DC)(DT)(DG)(DG)(DC)(DT)(DT)(DC)(DA) (DC)(DA)(
DC)(DT)(DT)(DG)(DA)(DT)(DT)(DT)(DG)(DC)(DA)(DT)(DC)(DA)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DA)(D
G)(DA)(DC)(DA)(DG)(DG)(DC)(DC)(DA)(DG)(DA)(DT)
Chain L
(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT)(DA)(DC)(DA)(DG)(DC)(DC)(DC)(DT)(DT)(DA)(DA) (DC)(DA)(
DA)(DA)(DA)(DA)(DC)(DC)(DC)(DG)
Chain J
(DA)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA)(DC)(DA)(DC)(DA)(DG) (DT)(DG)(
DA)(DT)(DG)(DC)(DA)(DA)(DA)(DT)(DC)(DA)(DA)(DG)(DT)(DG)(DT)(DG)(DA)(DA) (DG)(DC)(DC)(DA)(D
G)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC)(DC)(DG)
Protein Sequence:
Click to show/hide 3 protein sequences
Chain A,C
VHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQ PAVCLAIRV
NTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLAS SVDEYPVDTIAKRFRYDS
ALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFS FTVMRITIEHGSQNVKVFEEPKPNSEL
CCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFR GTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQ
NLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKP FIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKR
WQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETV DAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFA
ELLSTKFKYRYEGKITNYFHKTLAHV PEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAH
NA
Chain N
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP PKGETKKKF
KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA AYR
Chain B,D
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATCSY KGSIDSDKH
QYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRS YMPSTQRTTEKWNSVADC
LPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL PLGTPAVNCTVLPGGISVSSAILTQTN
NDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWFGS NMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLS
EDQ
Primary Citation:
Kim, M.S., Chuenchor, W., Chen, X., Cui, Y., Zhang, X., Zhou, Z.H., Gellert, M., Yang, W.
Cracking the DNA Code for V(D)J Recombination. 
Mol. Cell, 70, pp. 358 - 370.e4, 2018.
Experimental Information:
X-RAY DIFFRACTION
Space Group:
C 1 2 1
Cell Constants:
a = 156.678 b = 123.562 c = 186.286 (Ångstroms)
α = 90.0 β = 105.6 γ = 90.0 (degrees)
Refinement:
The structure was refined using the PHENIX program.
The R value is 0.216 for 39678 reflections in
the resolution range 38.693 to 3.6 Ångstroms
with Fobs > 1.35 sigma(Fobs) and with I > 0.0 sigma(I)