9LQV: VJ recombination-activating protein 1

Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1). Determined by electron microscopy at 3.1 Å resolution. Released 5 Aug 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Mus musculus, synthetic construct
Chains: 10
Atoms: 16,240
Mol. weight: 378.97 kDa
Ligands: ZN, MG
Released: 5 Aug 2026

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

Secondary structure: helices and β-sheets

9LQV contains 66 α-helices and 116 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	470-473	4
α-helix	478-492	15
α-helix	500-510	11
β-strand	518-519	2	1
α-helix	522-523	2
β-strand	534-536	3	2
β-strand	555-557	3	2
α-helix	559-569	11
α-helix	571-580	10
β-strand	590	1	3
β-strand	592-603	12	2
β-strand	618-631	14	2
β-strand	638-642	5	2
β-strand	653-658	6	2
α-helix	665-682	18
β-strand	687-688	2	1
β-strand	690-691	2	4
β-strand	694-695	2	4
β-strand	697	1	3
β-strand	698	1	1
β-strand	700	1	2
β-strand	706	1	2
α-helix	709-716	8
β-strand	725	1	5
β-strand	733	1	5
α-helix	734-740	7
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	825-840	16
α-helix	851-857	7
α-helix	860-867	8
α-helix	873-894	22
α-helix	898-901	4
α-helix	903-922	20
α-helix	934-941	8
α-helix	943-950	8
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-995	13
α-helix	997-1002	6

Chain B: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	7-8	2	7
α-helix	12-14	3
β-strand	20-23	4	7
β-strand	28-31	4	7
β-strand	45-51	7	7
β-strand	54-59	6	7
α-helix	61	1
β-strand	62	1	8
α-helix	63	1
α-helix	69-71	3
β-strand	73	1	9
β-strand	76-80	5	8
β-strand	90-94	5	8
β-strand	97	1	9
β-strand	103	1	9
β-strand	107-116	10	8
β-strand	119-127	9	8
α-helix	133-135	3
β-strand	138	1	10
β-strand	144-145	2	11
β-strand	152-156	5	11
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	181-185	5	11
β-strand	187	1	12
β-strand	189	1	12
β-strand	193-196	4	11
β-strand	205-212	8	13
β-strand	215-222	8	13
β-strand	223	1	14
β-strand	228	1	14
β-strand	233-234	2	15
β-strand	235-239	5	13
β-strand	246-248	3	13
β-strand	251-252	2	15
β-strand	259	1	16
β-strand	262-267	6	17
β-strand	270-274	5	17
β-strand	277	1	16
β-strand	279	1	18
β-strand	282	1	18
β-strand	288-291	4	17
β-strand	298-301	4	17
α-helix	302-305	4
α-helix	309-313	5
β-strand	318-321	4	6
β-strand	326-332	7	6
β-strand	337-343	7	6

Chain C: 24 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	500-510	11
β-strand	519	1	19
α-helix	522-523	2
β-strand	534-536	3	19
β-strand	555-557	3	19
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-602	12	19
β-strand	619-631	13	19
β-strand	639-642	4	19
β-strand	653-658	6	19
α-helix	665-682	18
β-strand	687	1	19
β-strand	690	1	20
β-strand	695	1	20
β-strand	698-704	7	19
α-helix	709-715	7
β-strand	718	1	21
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	21
β-strand	787	1	19
α-helix	793-812	20
α-helix	823-841	19
α-helix	851-857	7
α-helix	860-867	8
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-923	21
α-helix	934-950	17
α-helix	959-974	16
α-helix	983-995	13
α-helix	997-1001	5
α-helix	1002-1004	3

Chain D: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	22
β-strand	7-8	2	23
α-helix	12-14	3
β-strand	15-24	10	24
β-strand	27-33	7	24
β-strand	38	1	25
β-strand	41	1	25
β-strand	46-50	5	23
β-strand	54-59	6	23
β-strand	61-62	2	26
β-strand	73	1	27
β-strand	76-79	4	28
β-strand	91-94	4	28
β-strand	97	1	27
β-strand	103	1	27
β-strand	107-110	4	28
β-strand	112-114	3	26
β-strand	121-122	2	26
β-strand	125-127	3	28
β-strand	130-131	2	29
α-helix	133-136	4
β-strand	138	1	30
β-strand	141-145	5	29
α-helix	147-149	3
β-strand	152-156	5	29
β-strand	159-161	3	30
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	30
α-helix	178-179	2
β-strand	182-185	4	29
β-strand	191-195	5	29
β-strand	205	1	31
β-strand	208-211	4	32
β-strand	215-219	5	32
β-strand	222	1	31
β-strand	223	1	33
β-strand	228	1	33
β-strand	233-238	6	32
β-strand	247-252	6	32
β-strand	262-265	4	34
β-strand	270-274	5	34
β-strand	277	1	35
β-strand	283	1	35
β-strand	287-291	5	34
β-strand	298-302	5	34
α-helix	303-304	2
α-helix	309-312	4
β-strand	318-321	4	22
β-strand	326-332	7	22
β-strand	337-343	7	22

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)
Early growth response protein 1,V(D)J recombination-activating protein 2	B, D	protein	457	Mus musculus	P08046 (AlphaFold model), P21784 (AlphaFold model)
Flanking DNA in target DNA bottom strand	I	DNA	59	synthetic construct
Flanking DNA in target DNA top strand	J	DNA	59	synthetic construct
23RSS integration strand	x	DNA	77	synthetic construct
23RSS top strand	M	DNA	45	synthetic construct
12RSS integration strand	y	DNA	66	synthetic construct
12RSS top strand	L	DNA	34	synthetic construct

Sequence of entity 1 (A, C), FASTA

>9LQV_1 V(D)J recombination-activating protein 1 (chains A, C)
GPKKISNCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCL
KVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKE
SKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLA
LRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQ
PLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFR
YDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEK
AVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAE
REAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEAS
QNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDI
GNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMMMNGNFARKLM
TQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAE
LLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQ
SKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

Sequence of entity 2 (B, D), FASTA

>9LQV_2 Early growth response protein 1,V(D)J recombination-activating protein 2 (chains B, D)
GPMERPYACPVESCDRRFSDSSNLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHT
GEKPFACDICGRKFARSDERKRHTKIHLRQKDGGGNGSGGSGMSLQMVTVGHNIALIQPG
FSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATC
SYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRY
GHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLIDFEFGCATSYILP
ELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGISV
SSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWF
GSNMGNGTIFLGIPGDNAFYFYTLRCSEEDLSEDQKI

Sequence of entity 3 (I), FASTA

>9LQV_3 Flanking DNA in target DNA bottom strand (chains I)
ATGGTCCCACGCTAACCTAATAGAATTCCCCGTTCATCTGACACACAGCGTGGGACCAG

Sequence of entity 4 (J), FASTA

>9LQV_4 Flanking DNA in target DNA top strand (chains J)
CTGGTCCCACGCTGTGTGTCAGATGAACGGGGAATTCTATTAGGTTAGCGTGGGACCAT

Sequence of entity 5 (x), FASTA

>9LQV_5 23RSS integration strand (chains x)
GGTCGAGGTTTTTGTACAGCCAGACAACAGCCTACTACCACTGTGCCCCGTTCATCTGAC
ACACAGCGTGGGACCAG

Sequence of entity 6 (M), FASTA

>9LQV_6 23RSS top strand (chains M)
CACAGTGGTAGTAGGCTGTTGTCTGGCTGTACAAAAACCTCGACC

Sequence of entity 7 (y), FASTA

>9LQV_7 12RSS integration strand (chains y)
GGTCGAGGTTTTTGTACAGCCTACTACCACTGTGCGGGGAATTCTATTAGGTTAGCGTGG
GACCAT

Sequence of entity 8 (L), FASTA

>9LQV_8 12RSS top strand (chains L)
CACAGTGGTAGTAGGCTGTACAAAAACCTCGACC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	3

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
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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