6XNY: VJ recombination-activating protein 1

Name: PDB 6XNY: Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-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 (Paired-Form). Determined by electron microscopy at 2.9 Å resolution. Released 26 Aug 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Mus musculus
Chains: 10
Atoms: 16,681
Mol. weight: 323.97 kDa
Ligands: MG, ZN
Released: 26 Aug 2020

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

Secondary structure: helices and β-sheets

6XNY contains 71 α-helices and 118 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: 27 helices, 16 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	519	1	1
α-helix	522-523	2
β-strand	534-536	3	1
β-strand	554-557	4	1
α-helix	559-580	22
β-strand	590-598	9	1
β-strand	601-603	3	1
β-strand	618-632	15	1
β-strand	637-642	6	1
β-strand	652-658	7	1
α-helix	665-682	18
β-strand	687	1	1
β-strand	691	1	2
β-strand	694	1	2
β-strand	697-702	6	1
α-helix	709-715	7
β-strand	718	1	3
β-strand	725	1	4
β-strand	733	1	4
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	3
α-helix	782-783	2
α-helix	793-813	21
α-helix	823-839	17
α-helix	851-857	7
α-helix	860-867	8
α-helix	873-894	22
α-helix	898-901	4
α-helix	903-906	4
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	997-1003	7

Chain B: 7 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
β-strand	7-8	2	6
α-helix	12-14	3
β-strand	15	1	7
β-strand	21-24	4	8
β-strand	27-30	4	8
β-strand	33	1	7
α-helix	37-38	2
β-strand	46-51	6	6
β-strand	54-59	6	6
β-strand	62	1	9
β-strand	73	1	10
β-strand	76-78	3	11
β-strand	91-94	4	11
β-strand	97	1	10
β-strand	103	1	10
β-strand	107-110	4	11
β-strand	114	1	12
β-strand	121	1	12
β-strand	122	1	9
β-strand	124-127	4	11
β-strand	130-131	2	13
α-helix	133-135	3
β-strand	138	1	14
β-strand	141	1	15
β-strand	144-146	3	15
β-strand	151-156	6	15
β-strand	159-161	3	14
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	14
β-strand	182-185	4	15
β-strand	186	1	13
β-strand	191-192	2	13
β-strand	208-212	5	16
β-strand	215-219	5	16
β-strand	223	1	17
β-strand	228	1	17
β-strand	233-234	2	18
β-strand	235-239	5	16
β-strand	246-248	3	16
β-strand	251-252	2	18
β-strand	262-267	6	19
β-strand	270-274	5	19
β-strand	277-279	3	20
β-strand	282-283	2	20
β-strand	289-292	4	19
β-strand	297-300	4	19
α-helix	302-304	3
α-helix	309-312	4
β-strand	318-321	4	5
β-strand	326-332	7	5
β-strand	343-349	7	5

Chain C: 30 helices, 16 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	21
α-helix	522-523	2
β-strand	534-536	3	21
β-strand	541	1	22
β-strand	554-557	4	21
α-helix	559-569	11
α-helix	571-579	9
β-strand	591-598	8	21
β-strand	601	1	21
β-strand	620-633	14	21
β-strand	636-642	7	21
β-strand	652-658	7	21
α-helix	665-682	18
β-strand	687-691	5	21
β-strand	694-704	11	21
α-helix	709-715	7
β-strand	716	1	23
β-strand	725	1	24
β-strand	733	1	24
α-helix	736-739	4
α-helix	750-762	13
α-helix	769-776	8
α-helix	782	1
β-strand	783	1	23
β-strand	787	1	21
α-helix	793-811	19
α-helix	823-839	17
α-helix	843-845	3
α-helix	853-856	4
α-helix	860-867	8
α-helix	873-889	17
α-helix	890-892	3
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-922	14
α-helix	925-928	4
α-helix	934-941	8
α-helix	943-950	8
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1003	7

Chain D: 7 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	25
β-strand	7-8	2	26
α-helix	12-14	3
β-strand	20-24	5	26
β-strand	27-31	5	26
β-strand	46-50	5	26
β-strand	54-59	6	26
β-strand	61-62	2	27
β-strand	73	1	28
β-strand	76-78	3	27
β-strand	91-94	4	27
β-strand	97	1	28
α-helix	102	1
β-strand	103	1	28
α-helix	104	1
β-strand	107-116	10	27
β-strand	119-127	9	27
β-strand	130-131	2	29
β-strand	137-138	2	30
β-strand	141-147	7	31
β-strand	150-156	7	31
β-strand	159-161	3	30
α-helix	162-163	2
α-helix	169-171	3
β-strand	174	1	22
β-strand	175-177	3	30
α-helix	178-179	2
β-strand	182-185	4	31
β-strand	191-192	2	29
β-strand	207-211	5	32
β-strand	215-220	6	32
β-strand	223	1	33
β-strand	228	1	33
β-strand	233-239	7	32
β-strand	246-252	7	32
β-strand	262	1	34
β-strand	267	1	35
β-strand	270-273	4	35
β-strand	274	1	34
β-strand	277-279	3	36
β-strand	282-283	2	36
β-strand	288-293	6	35
β-strand	296-299	4	35
α-helix	309-312	4
β-strand	318-321	4	25
β-strand	327-332	6	25
β-strand	343-349	7	25

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 (55-mer)	x	DNA	55	Mus musculus
23RSS integration strand (66-mer)	y	DNA	66	Mus musculus
Flanking DNA top strand (16-mer)	I, J	DNA	16	Mus musculus
23RSS signal DNA top strand (45-mer)	L	DNA	45	Mus musculus
12RSS signal DNA top strand (34-mer)	M	DNA	34	Mus musculus

Sequence of entity 1 (A, C), FASTA

>6XNY_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

>6XNY_2 V(D)J recombination-activating protein 2 (chains B, D)
GPMALQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLK
PAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNK
KVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADC
LPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRV
DLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIE
ISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSED
QKI

Sequence of entity 3 (x), FASTA

>6XNY_3 12RSS integration strand (55-mer) (chains x)
GGTCGAGGTTTTTGTACAGCCTACTACCACTGTGCGCCGGTAGCCCTATCCTGAG

Sequence of entity 4 (y), FASTA

>6XNY_4 23RSS integration strand (66-mer) (chains y)
GGTCGAGGTTTTTGTACAGCCAGACAACAGCCTACTACCACTGTGCGGCGGTAGCCCTAT
CCTGAG

Sequence of entity 5 (I, J), FASTA

>6XNY_5 Flanking DNA top strand (16-mer) (chains I, J)
CTCAGGATAGGGCTAC

Sequence of entity 6 (L), FASTA

>6XNY_6 23RSS signal DNA top strand (45-mer) (chains L)
CACAGTGGTAGTAGGCTGTTGTCTGGCTGTACAAAAACCTCGACC

Sequence of entity 7 (M), FASTA

>6XNY_7 12RSS signal DNA top strand (34-mer) (chains M)
CACAGTGGTAGTAGGCTGTACAAAAACCTCGACC

Ligands and cofactors

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

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
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+
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)

Browse structure collections

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