9JPU: Mouse RAG SEC-PHD

CryoEM structure of mouse RAG SEC-PHD. Determined by electron microscopy at 3.25 Å resolution. Released 23 Jul 2025.

Method: Electron microscopy
Resolution: 3.25 Å
Organisms: Mus musculus, Escherichia coli
Chains: 9
Atoms: 15,963
Mol. weight: 434.27 kDa
Ligands: CA, ZN
Released: 23 Jul 2025

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

Secondary structure: helices and β-sheets

9JPU contains 72 α-helices and 104 β-strands across 5 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: 26 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-506	7
β-strand	517-520	4	1
α-helix	522-523	2
β-strand	535-536	2	2
β-strand	554-556	3	2
α-helix	559-580	22
β-strand	591-601	11	2
β-strand	620-632	13	2
β-strand	637-642	6	2
β-strand	653-658	6	2
α-helix	665-681	17
β-strand	686-690	5	1
β-strand	695-698	4	1
β-strand	700-704	5	2
α-helix	709-715	7
β-strand	718	1	3
β-strand	725	1	4
β-strand	733	1	4
α-helix	734-740	7
α-helix	750-762	13
α-helix	769-775	7
β-strand	779	1	3
α-helix	793-811	19
α-helix	825-840	16
α-helix	851-857	7
α-helix	860-866	7
α-helix	867-869	3
α-helix	873-889	17
α-helix	890-892	3
α-helix	898-901	4
α-helix	903-907	5
α-helix	910-922	13
α-helix	934-941	8
α-helix	944-950	7
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1003	7

Chain B: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	5
β-strand	7-8	2	6
α-helix	12-14	3
β-strand	20-24	5	6
β-strand	27-31	5	6
β-strand	45-51	7	6
β-strand	54-59	6	6
β-strand	62	1	7
β-strand	76-80	5	7
β-strand	90-94	5	7
β-strand	97	1	8
β-strand	103	1	8
β-strand	107-116	10	7
β-strand	119-127	9	7
β-strand	130-131	2	9
α-helix	133-135	3
β-strand	138	1	10
β-strand	142-147	6	9
β-strand	150-155	6	9
β-strand	159-161	3	10
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	10
α-helix	178-179	2
β-strand	182-186	5	9
β-strand	191-195	5	9
β-strand	208-211	4	11
β-strand	215-219	5	11
β-strand	223	1	12
β-strand	228	1	12
β-strand	233-239	7	11
β-strand	246-252	7	11
β-strand	262-267	6	13
β-strand	270-274	5	13
β-strand	277	1	14
β-strand	283	1	14
β-strand	288-292	5	13
β-strand	297-301	5	13
α-helix	303-305	3
α-helix	309-312	4
β-strand	318-321	4	5
β-strand	326-330	5	5
β-strand	332	1	15
β-strand	343	1	15
β-strand	346-349	4	5

Chain C: 29 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-506	7
α-helix	507-509	3
β-strand	518-519	2	16
α-helix	522-523	2
β-strand	535-536	2	16
β-strand	554-556	3	16
α-helix	559-568	10
α-helix	571-580	10
β-strand	590-601	12	16
β-strand	620-633	14	16
β-strand	636-642	7	16
β-strand	653-658	6	16
α-helix	665-683	19
β-strand	687-691	5	16
β-strand	694-704	11	16
α-helix	709-715	7
β-strand	718	1	17
α-helix	719	1
β-strand	725	1	18
β-strand	733	1	18
α-helix	734-740	7
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	17
α-helix	787-789	3
α-helix	793-812	20
α-helix	823-841	19
α-helix	851-857	7
α-helix	860-867	8
α-helix	873-894	22
α-helix	898-901	4
α-helix	903-907	5
α-helix	910-922	13
α-helix	934-937	4
α-helix	938-942	5
α-helix	943-949	7
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1003	7

Chain D: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
β-strand	7	1	20
α-helix	12-14	3
β-strand	20-24	5	20
β-strand	27-31	5	20
β-strand	46-51	6	20
β-strand	54-59	6	20
β-strand	61-62	2	21
α-helix	69-71	3
β-strand	76-80	5	21
β-strand	90-94	5	21
β-strand	97	1	22
β-strand	103	1	22
β-strand	107-116	10	21
β-strand	119-127	9	21
β-strand	130-131	2	23
α-helix	133-136	4
β-strand	138	1	24
β-strand	142-147	6	23
β-strand	150-155	6	23
β-strand	159-161	3	24
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	24
α-helix	178-179	2
β-strand	182-186	5	23
β-strand	191-195	5	23
β-strand	208-211	4	25
β-strand	215-219	5	25
β-strand	223	1	26
β-strand	228	1	26
β-strand	233-239	7	25
β-strand	246-252	7	25
β-strand	259	1	27
β-strand	262-264	3	28
β-strand	270-274	5	28
β-strand	277-279	3	27
β-strand	282-283	2	27
β-strand	288-291	4	28
β-strand	298-301	4	28
α-helix	303-305	3
α-helix	309-312	4
β-strand	318-321	4	19
β-strand	326-331	6	19
β-strand	344-349	6	19

Chain E: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	443-446	4	29
β-strand	452-455	4	29
α-helix	457-459	3
α-helix	463-469	7

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, E	protein	527	Mus musculus	P21784 (AlphaFold model)
DNA (5'-d(pgpgpcptpgptpaptpcpapcptpgptp*g)-3')	F	DNA	15	Escherichia coli
DNA (5'-d(ptptptpgpcpaptpcpapcptpgptpg)-3')	G	DNA	14	Escherichia coli
DNA (5'-d(cpapcpapgptpgpaptpapcpapgpcp*c)-3')	L	DNA	15	Escherichia coli
DNA (5'-d(cpapcpapgptpgpaptpgpcpapapa)-3')	M	DNA	14	Escherichia coli

Sequence of entity 1 (A, C), FASTA

>9JPU_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, E), FASTA

>9JPU_2 V(D)J recombination-activating protein 2 (chains B, D, E)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQK
IVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCC
PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNE
HVQIARALQTPKRNPPLQKPPMKSLHKKGSGKVLTPAKKSFLRRLFD

Sequence of entity 3 (F), FASTA

>9JPU_3 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 4 (G), FASTA

>9JPU_4 DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') (chains G)
TTTGCATCACTGTG

Sequence of entity 5 (L), FASTA

>9JPU_5 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 6 (M), FASTA

>9JPU_6 DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3') (chains M)
CACAGTGATGCAAA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	4

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)
9JQN 3.03 Å, CryoEM structure of mouse RAG SEC-2DNA
6OES 3.06 Å, Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)

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