6XNX: VJ recombination-activating protein 1

Name: PDB 6XNX: Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)
Published: 2020-08-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: recombination

Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form). Determined by electron microscopy at 2.7 Å resolution. Released 26 Aug 2020.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Mus musculus, Homo sapiens
Chains: 10
Atoms: 16,540
Mol. weight: 323.97 kDa
Ligands: ZN, MG
Released: 26 Aug 2020

Explore 6XNX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XNX contains 72 α-helices and 117 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: 30 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	461-463	3
α-helix	464-473	10
α-helix	478-491	14
α-helix	498-499	2
α-helix	500-510	11
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	590-602	13	1
α-helix	606-609	4
β-strand	619-631	13	1
β-strand	639-642	4	1
β-strand	652-658	7	1
α-helix	665-682	18
β-strand	687-691	5	1
β-strand	694-702	9	1
β-strand	704	1	2
α-helix	709-715	7
β-strand	718	1	3
α-helix	719-720	2
β-strand	725	1	4
β-strand	733	1	4
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-775	7
β-strand	779	1	3
β-strand	787	1	2
α-helix	793-812	20
α-helix	825-839	15
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	909-922	14
α-helix	934-937	4
α-helix	938-942	5
α-helix	943-950	8
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1002	6

Chain B: 6 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	5-6	2	6
β-strand	7-8	2	7
α-helix	12-14	3
β-strand	15	1	8
β-strand	21-24	4	7
β-strand	27-30	4	7
β-strand	33	1	8
β-strand	46-51	6	7
β-strand	54-59	6	7
β-strand	61-62	2	9
β-strand	73	1	10
β-strand	76-80	5	11
β-strand	90-94	5	11
β-strand	97	1	10
β-strand	103	1	10
β-strand	107-110	4	11
β-strand	113	1	9
β-strand	121-122	2	9
β-strand	124-127	4	11
β-strand	130-131	2	12
α-helix	133-135	3
β-strand	138	1	13
β-strand	141	1	12
β-strand	144-145	2	12
β-strand	152-156	5	12
β-strand	159-161	3	13
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	13
β-strand	181	1	14
β-strand	182-186	5	12
β-strand	191-193	3	12
β-strand	196	1	14
β-strand	208-212	5	15
β-strand	215-219	5	15
β-strand	223	1	16
β-strand	228	1	16
β-strand	235-239	5	15
β-strand	246-248	3	15
α-helix	251-252	2
β-strand	262-264	3	17
β-strand	270-274	5	17
β-strand	277	1	18
β-strand	283	1	18
β-strand	288-293	6	17
β-strand	296-299	4	17
α-helix	309-312	4
β-strand	318-321	4	6
β-strand	327-332	6	6
β-strand	343-348	6	6
β-strand	349	1	5

Chain C: 28 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-491	14
α-helix	498-499	2
α-helix	500-510	11
β-strand	517-519	3	19
α-helix	522-523	2
β-strand	534-536	3	19
β-strand	541	1	20
β-strand	554-557	4	19
α-helix	559-580	22
β-strand	591-601	11	19
α-helix	606-608	3
β-strand	620-633	14	19
β-strand	636-642	7	19
β-strand	652-658	7	19
α-helix	665-683	19
β-strand	687-691	5	19
β-strand	694-704	11	19
α-helix	709-715	7
α-helix	718-720	3
β-strand	725	1	21
β-strand	733	1	21
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
β-strand	787	1	19
α-helix	793-813	21
α-helix	823-839	17
α-helix	843-845	3
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	909-922	14
α-helix	934-937	4
α-helix	938-942	5
α-helix	943-950	8
α-helix	959-974	16
α-helix	980-994	15
α-helix	997-1003	7

Chain D: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	22
β-strand	7	1	23
α-helix	12-14	3
β-strand	15	1	24
β-strand	22-24	3	23
β-strand	27-30	4	23
β-strand	33	1	24
α-helix	37-38	2
β-strand	46-51	6	23
β-strand	54-59	6	23
β-strand	61-62	2	25
β-strand	73	1	26
β-strand	76-79	4	25
α-helix	90	1
β-strand	91-94	4	25
β-strand	97-98	2	26
β-strand	102-103	2	26
α-helix	104	1
β-strand	107-116	10	25
β-strand	119-127	9	25
β-strand	130-131	2	27
β-strand	138	1	28
β-strand	141-147	7	27
β-strand	150-156	7	27
β-strand	159-161	3	28
α-helix	162-163	2
α-helix	169-171	3
β-strand	174	1	20
β-strand	175-177	3	28
α-helix	178-179	2
β-strand	181	1	29
β-strand	182-185	4	27
β-strand	191-193	3	27
β-strand	196	1	29
β-strand	208-211	4	30
β-strand	215-219	5	30
β-strand	223	1	31
β-strand	228	1	31
β-strand	233-239	7	30
β-strand	246-252	7	30
β-strand	259	1	32
β-strand	262-267	6	33
β-strand	270-274	5	33
β-strand	277-279	3	32
β-strand	282-283	2	32
β-strand	288-292	5	33
β-strand	297-301	5	33
α-helix	309-312	4
β-strand	318-321	4	22
β-strand	326-332	7	22
β-strand	343-349	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)
V(D)J recombination-activating protein 2	B, D	protein	363	Mus musculus	P21784 (AlphaFold model)
12RSS integration strand DNA (55-MER)	x	DNA	55	Homo sapiens
23RSS integration strand DNA (66-MER)	y	DNA	66	Homo sapiens
Flanking DNA top strand DNA	I, J	DNA	16	Homo sapiens
23RSS signal top strand DNA (45-MER)	L	DNA	45	Homo sapiens
12RSS signal top strand DNA (34-MER)	M	DNA	34	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>6XNX_1 V(D)J recombination-activating protein 1 (chains A, C)
GPKKISNCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCL
KVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKE
SKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLA
LRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQ
PLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFR
YDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEK
AVRFSFTVMRITIEHGSQNVKVFEEPKPNSVLCCKPLCLMLADESDHETLTAILSPLIAE
REAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEAS
QNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDI
GNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMMMNGNFARKLM
TQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAE
LLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQ
SKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

Sequence of entity 2 (B, D), FASTA

>6XNX_2 V(D)J recombination-activating protein 2 (chains B, D)
GPMALQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLK
PAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNK
KVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADC
LPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRV
DLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIE
ISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSED
QKI

Sequence of entity 3 (x), FASTA

>6XNX_3 12RSS integration strand DNA (55-MER) (chains x)
GGTCGAGGTTTTTGTACAGCCTACTACCACTGTGCGCCGGTAGCCCTATCCTGAG

Sequence of entity 4 (y), FASTA

>6XNX_4 23RSS integration strand DNA (66-MER) (chains y)
GGTCGAGGTTTTTGTACAGCCAGACAACAGCCTACTACCACTGTGCGGCGGTAGCCCTAT
CCTGAG

Sequence of entity 5 (I, J), FASTA

>6XNX_5 Flanking DNA top strand DNA (chains I, J)
CTCAGGATAGGGCTAC

Sequence of entity 6 (L), FASTA

>6XNX_6 23RSS signal top strand DNA (45-MER) (chains L)
CACAGTGGTAGTAGGCTGTTGTCTGGCTGTACAAAAACCTCGACC

Sequence of entity 7 (M), FASTA

>6XNX_7 12RSS signal top strand DNA (34-MER) (chains M)
CACAGTGGTAGTAGGCTGTACAAAAACCTCGACC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	4

Primary citation

Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. Zhang, Y., Corbett, E., Wu, S. et al. EMBO J (2020) 39:e105857-e105857. DOI 10.15252/embj.2020105857 · 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
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)
9LQV 3.1 Å, Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)

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