9LQO: RAG transposon end complex

Structure of RAG transposon end complex (TEC). Determined by electron microscopy at 3.0 Å resolution. Released 5 Aug 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Mus musculus, synthetic construct
Chains: 8
Atoms: 15,225
Mol. weight: 300.94 kDa
Ligands: MG, ZN
Released: 5 Aug 2026

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

Secondary structure: helices and β-sheets

9LQO contains 66 α-helices and 104 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: 26 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	500-509	10
β-strand	518-519	2	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
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	694-707	14	1
α-helix	709-715	7
β-strand	718	1	2
α-helix	719	1
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	2
α-helix	793-812	20
α-helix	823-840	18
α-helix	852-857	6
α-helix	860-867	8
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-923	15
α-helix	934-941	8
α-helix	943-949	7
α-helix	959-974	16
α-helix	980-994	15
α-helix	997-1003	7

Chain B: 6 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	7-8	2	4
β-strand	20-23	4	4
β-strand	28-31	4	4
β-strand	46-50	5	4
β-strand	54-59	6	4
β-strand	62	1	5
β-strand	76-80	5	5
β-strand	90-94	5	5
β-strand	97	1	6
β-strand	103	1	6
β-strand	107-114	8	5
β-strand	121-127	7	5
β-strand	130-131	2	7
α-helix	133-135	3
β-strand	138	1	8
β-strand	141-146	6	7
β-strand	151-156	6	7
β-strand	159-161	3	8
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	8
α-helix	178-179	2
β-strand	181-186	6	7
β-strand	191-196	6	7
β-strand	208-211	4	9
β-strand	215-219	5	9
β-strand	223	1	10
β-strand	228	1	10
β-strand	233-239	7	9
β-strand	246-252	7	9
β-strand	259	1	11
β-strand	262-267	6	12
β-strand	270-274	5	12
β-strand	277-279	3	11
β-strand	282-283	2	11
β-strand	288-292	5	12
β-strand	297-301	5	12
α-helix	303-305	3
α-helix	309-313	5
β-strand	318-321	4	3
β-strand	326-332	7	3
β-strand	343-349	7	3

Chain C: 28 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	500-510	11
β-strand	518-519	2	13
α-helix	522-523	2
β-strand	534-536	3	13
β-strand	554-557	4	13
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-602	12	13
α-helix	606-608	3
β-strand	619-633	15	13
β-strand	636-642	7	13
β-strand	653-658	6	13
α-helix	665-682	18
β-strand	687-691	5	13
β-strand	694-707	14	13
α-helix	709-715	7
β-strand	718	1	14
α-helix	719	1
β-strand	725	1	15
β-strand	733	1	15
α-helix	734-740	7
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	14
α-helix	793-811	19
α-helix	823-840	18
α-helix	851-857	7
α-helix	860-867	8
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-923	15
α-helix	925-928	4
α-helix	934-950	17
α-helix	954-956	3
α-helix	959-974	16
α-helix	980-994	15
α-helix	997-1002	6

Chain D: 6 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	16
β-strand	6	1	16
β-strand	7-8	2	17
α-helix	12-14	3
β-strand	20-23	4	17
β-strand	28-31	4	17
β-strand	46-50	5	17
β-strand	54-59	6	17
β-strand	61-62	2	18
β-strand	75-80	6	18
β-strand	90-95	6	18
β-strand	97	1	19
β-strand	103	1	19
β-strand	107-116	10	18
β-strand	119-127	9	18
β-strand	130-131	2	20
α-helix	133-136	4
β-strand	138	1	21
β-strand	142-147	6	22
β-strand	150-155	6	22
β-strand	159-161	3	21
α-helix	169-171	3
β-strand	175-177	3	21
α-helix	178-179	2
β-strand	181-185	5	22
β-strand	186	1	20
β-strand	191-192	2	20
β-strand	194-196	3	22
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	246-252	7	24
β-strand	259	1	26
β-strand	262-267	6	27
β-strand	270-274	5	27
β-strand	277-279	3	26
β-strand	282-283	2	26
β-strand	287-292	6	27
β-strand	297-301	5	27
α-helix	302-305	4
α-helix	309-312	4
β-strand	318-321	4	16
β-strand	326-332	7	16
β-strand	343-345	3	16
β-strand	348-349	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A, C	protein	750	Mus musculus	P15919 (AlphaFold model)
V(D)J recombination-activating protein 2	B, D	protein	363	Mus musculus	P21784 (AlphaFold model)
12RSS bottom strand	F	DNA	34	synthetic construct
12RSS top strand	L	DNA	34	synthetic construct
23RSS bottom strand	G	DNA	45	synthetic construct
23RSS top strand	M	DNA	45	synthetic construct

Sequence of entity 1 (A, C), FASTA

>9LQO_1 V(D)J recombination-activating protein 1 (chains A, C)
GPKKISNCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCL
KVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKE
SKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLA
LRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQ
PLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFR
YDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEK
AVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADASDHETLTAILSPLIAE
REAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEAAGAVYICTLCDTTRLEAS
QNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDI
GNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMMMNGNFARKLM
TQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAE
LLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQ
SKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

Sequence of entity 2 (B, D), FASTA

>9LQO_2 V(D)J recombination-activating protein 2 (chains B, D)
GPMSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLE
PAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNK
AVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADC
LPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRV
DLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIE
ISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSED
QKI

Sequence of entity 3 (F), FASTA

>9LQO_3 12RSS bottom strand (chains F)
GGTCGAGGTTTTTGTACAGCCTACTACCACTGTG

Sequence of entity 4 (L), FASTA

>9LQO_4 12RSS top strand (chains L)
CACAGTGGTAGTAGGCTGTACAAAAACCTCGACC

Sequence of entity 5 (G), FASTA

>9LQO_5 23RSS bottom strand (chains G)
GGTCGAGGTTTTTGTACAGCCAGACAACAGCCTACTACCACTGTG

Sequence of entity 6 (M), FASTA

>9LQO_6 23RSS top strand (chains M)
CACAGTGGTAGTAGGCTGTTGTCTGGCTGTACAAAAACCTCGACC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Primary citation

Structural basis and dynamics of target capture and integration during cut-and-paste transposition. Pang, J., Martin, E.C., Zheng, X. et al. To be published.

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
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)
9LQV 3.1 Å, Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)

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