9JQN: Mouse RAG SEC-2DNA

CryoEM structure of mouse RAG SEC-2DNA. Determined by electron microscopy at 3.03 Å resolution. Released 23 Jul 2025.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Mus musculus, Escherichia coli
Chains: 12
Atoms: 16,485
Mol. weight: 391.51 kDa
Ligands: CA, ZN
Released: 23 Jul 2025

Explore 9JQN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JQN contains 66 α-helices and 101 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-507	8
β-strand	517-519	3	1
α-helix	522-523	2
β-strand	534-536	3	1
β-strand	554-557	4	1
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-602	12	1
α-helix	605-607	3
β-strand	619-633	15	1
β-strand	636-642	7	1
β-strand	653-658	6	1
α-helix	665-682	18
β-strand	687-691	5	1
β-strand	694-706	13	1
α-helix	709-715	7
β-strand	725	1	2
β-strand	733	1	2
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-813	21
α-helix	823-841	19
α-helix	851-857	7
α-helix	860-867	8
α-helix	874-889	16
α-helix	890-892	3
α-helix	903-923	21
α-helix	934-941	8
α-helix	943-950	8
α-helix	959-974	16
α-helix	983-995	13
α-helix	1005-1007	3

Chain B: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	3
β-strand	7	1	4
α-helix	12-14	3
β-strand	20-24	5	5
β-strand	27-31	5	5
β-strand	46-50	5	5
β-strand	54	1	4
β-strand	55-59	5	5
β-strand	62	1	6
β-strand	76-78	3	6
β-strand	90-94	5	6
β-strand	97	1	7
β-strand	103	1	7
β-strand	107-116	10	6
β-strand	119-127	9	6
β-strand	130-131	2	8
α-helix	133-135	3
β-strand	138	1	9
β-strand	142-147	6	8
β-strand	150-155	6	8
β-strand	159-161	3	9
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	9
α-helix	178-179	2
β-strand	182-186	5	8
β-strand	191-195	5	8
β-strand	205	1	10
β-strand	208-211	4	11
β-strand	215-219	5	11
β-strand	222	1	10
β-strand	223	1	12
β-strand	228	1	12
β-strand	233-239	7	11
β-strand	246-251	6	11
β-strand	259	1	13
β-strand	262-267	6	14
β-strand	270-274	5	14
β-strand	277	1	13
β-strand	283	1	13
β-strand	288-292	5	14
β-strand	297-301	5	14
α-helix	303-305	3
α-helix	309-312	4
β-strand	318-321	4	3
β-strand	326-332	7	3
α-helix	336-338	3
β-strand	343-349	7	3

Chain C: 28 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-510	11
β-strand	517-520	4	15
α-helix	522-523	2
β-strand	535-536	2	15
β-strand	554-556	3	15
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-603	13	15
α-helix	605-608	4
β-strand	618-633	16	15
β-strand	636-642	7	15
β-strand	653-658	6	15
α-helix	666-682	17
β-strand	686-691	6	15
β-strand	694-706	13	15
α-helix	709-715	7
β-strand	725	1	16
β-strand	733	1	16
α-helix	734-740	7
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-841	19
α-helix	851-857	7
α-helix	860-866	7
α-helix	873-894	22
α-helix	898-900	3
α-helix	903-907	5
α-helix	909-922	14
α-helix	934-941	8
α-helix	943-949	7
α-helix	954-956	3
α-helix	959-974	16
α-helix	984-994	11
α-helix	997-1000	4
α-helix	1001-1003	3

Chain D: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
β-strand	7-8	2	18
α-helix	12-14	3
β-strand	20-24	5	18
β-strand	27-31	5	18
β-strand	46-51	6	18
β-strand	54-59	6	18
β-strand	61-62	2	19
β-strand	76-78	3	19
β-strand	91-94	4	19
β-strand	97	1	20
β-strand	103	1	20
β-strand	107-116	10	19
β-strand	119-127	9	19
β-strand	130-131	2	21
α-helix	133-135	3
β-strand	138	1	22
β-strand	142-147	6	21
β-strand	150-155	6	21
β-strand	159-161	3	22
α-helix	162-163	2
β-strand	175-177	3	22
α-helix	178-179	2
β-strand	182-186	5	21
β-strand	191-195	5	21
β-strand	205	1	23
β-strand	208-211	4	24
β-strand	215-219	5	24
β-strand	222	1	23
β-strand	223	1	25
β-strand	228	1	25
β-strand	233-239	7	24
β-strand	246-251	6	24
β-strand	259	1	26
β-strand	262-267	6	27
β-strand	270-274	5	27
β-strand	277	1	26
β-strand	283	1	26
β-strand	288-291	4	27
β-strand	298-301	4	27
α-helix	303-305	3
α-helix	309-312	4
β-strand	318-321	4	17
β-strand	326-332	7	17
β-strand	343-349	7	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A, C	protein	1040	Mus musculus	P15919 (AlphaFold model)
V(D)J recombination-activating protein 2	B, D	protein	527	Mus musculus	P21784 (AlphaFold model)
DNA (5'-d(paptptptpgpcpaptpcpapcptpgptp*g)-3')	G	DNA	15	Escherichia coli
DNA (5'-d(cpapcpapgptpgpaptpapcpapgpcp*c)-3')	L	DNA	15	Escherichia coli
DNA (5'-d(cpapcpapgptpgpaptpgpcpapapap*t)-3')	M	DNA	15	Escherichia coli
DNA (5'-d(pgpgpcptpgptpaptpcpapcptpgptp*g)-3')	F	DNA	15	Escherichia coli
DNA (5'-d(cpapgpgpcpcpapgpaptpcpcp*a)-3')	E, H	DNA	13	Escherichia coli
DNA (5'-d(ptpgpgpaptpcptpgpgpcpcptp*g)-3')	I, J	DNA	13	Escherichia coli

Sequence of entity 1 (A, C), FASTA

>9JQN_1 V(D)J recombination-activating protein 1 (chains A, C)
MAASLPSTLSFSSAPDEIQHPQIKFSEWKFKLFRVRSFEKAPEEAQKEKDSSEGKPYLEQ
SPVVPEKPGGQNSILTQRALKLHPKFSKKFHADGKSSDKAVHQARLRHFCRICGNRFKSD
GHSRRYPVHGPVDAKTQSLFRKKEKRVTSWPDLIARIFRIDVKADVDSIHPTEFCHDCWS
IMHRKFSSSHSQVYFPRKVTVEWHPHTPSCDICFTAHRGLKRKRHQPNVQLSKKLKTVLN
HARRDRRKRTQARVSSKEVLKKISNCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADP
VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDC
NEEVSLEKYNHHVSSHKESKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFAD
KEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQ
YHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSG
LASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCD
GMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLA
DESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEA
SGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVS
AKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKR
MNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAK
ECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEG
NESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNALKSSGFTMNSKE
TLGDPLGIEDSLESQDSMEF

Sequence of entity 2 (B, D), FASTA

>9JQN_2 V(D)J recombination-activating protein 2 (chains B, D)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQK
IVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCC
PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNE
HVQIARALQTPKRNPPLQKPPMKSLHKKGSGKVLTPAKKSFLRRLFD

Sequence of entity 3 (G), FASTA

>9JQN_3 DNA (5'-D(P*AP*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') (chains G)
ATTTGCATCACTGTG

Sequence of entity 4 (L), FASTA

>9JQN_4 DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3') (chains L)
CACAGTGATACAGCC

Sequence of entity 5 (M), FASTA

>9JQN_5 DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*AP*T)-3') (chains M)
CACAGTGATGCAAAT

Sequence of entity 6 (F), FASTA

>9JQN_6 DNA (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') (chains F)
GGCTGTATCACTGTG

Sequence of entity 7 (E, H), FASTA

>9JQN_7 DNA (5'-D(*CP*AP*GP*GP*CP*CP*AP*GP*AP*TP*CP*CP*A)-3') (chains E, H)
CAGGCCAGATCCA

Sequence of entity 8 (I, J), FASTA

>9JQN_8 DNA (5'-D(P*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3') (chains I, J)
TGGATCTGGCCTG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	2

Primary citation

How RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination without transposition. Chen, X., Yao, L., Li, W. et al. Proc Natl Acad Sci U S A (2025) 122:e2512362122-e2512362122. DOI 10.1073/pnas.2512362122 · PubMed

Other PDB entries of the same protein (UniProt P15919 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RMD 2.1 Å, RAG1 dimerization domain
3GNA 2.4 Å, Crystal structure of the RAG1 nonamer-binding domain with DNA
6XNX 2.7 Å, Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)
5ZE0 2.75 Å, Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+
5ZDZ 2.8 Å, Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+
6XNY 2.9 Å, Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form)
9JPX 2.95 Å, CryoEM structure of mouse RAG SEC-0
3GNB 3.0 Å, Crystal structure of the RAG1 nonamer-binding domain with DNA
5ZE1 3.0 Å, Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C
9LQO 3.0 Å, Structure of RAG transposon end complex (TEC)
6OES 3.06 Å, Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)
9LQV 3.1 Å, Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)

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