6CIM: VJ recombination-activating protein 1

Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+. Determined by X-ray diffraction at 3.6 Å resolution. Released 25 Apr 2018.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Mus musculus, Homo sapiens
Chains: 10
Atoms: 18,804
Mol. weight: 301.73 kDa
Ligands: ZN, MN
Released: 25 Apr 2018

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

Secondary structure: helices and β-sheets

6CIM contains 91 α-helices and 102 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: 31 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	396-398	3
α-helix	401-422	22
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-474	11
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-510	11
β-strand	517-520	4	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
α-helix	590	1
β-strand	591-604	14	1
β-strand	618-632	15	1
β-strand	637-642	6	1
β-strand	653-658	6	1
α-helix	665-682	18
β-strand	686-691	6	1
β-strand	694-706	13	1
α-helix	709-715	7
α-helix	718-720	3
β-strand	725	1	2
β-strand	733	1	2
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-840	18
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	962-974	13
α-helix	980-995	16
α-helix	997-1003	7

Chain B: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	7-8	2	4
α-helix	12-14	3
β-strand	20-24	5	4
β-strand	27-31	5	4
β-strand	45-51	7	4
β-strand	54-59	6	4
β-strand	61-62	2	5
α-helix	69-71	3
β-strand	73	1	6
β-strand	76-80	5	5
β-strand	90-94	5	5
β-strand	97	1	6
α-helix	102	1
β-strand	103	1	6
α-helix	104	1
β-strand	107-115	9	5
β-strand	120-127	8	5
β-strand	130-131	2	7
α-helix	133-136	4
β-strand	138	1	8
β-strand	141-147	7	7
β-strand	150-156	7	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	205	1	9
β-strand	208-212	5	10
β-strand	215-219	5	10
β-strand	222	1	9
β-strand	223	1	11
β-strand	228	1	11
β-strand	233-239	7	10
β-strand	246-252	7	10
β-strand	259	1	12
β-strand	262-267	6	13
β-strand	270-274	5	13
β-strand	277	1	12
β-strand	283	1	12
β-strand	287-292	6	13
β-strand	297-302	6	13
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: 31 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	401-407	7
α-helix	409-423	15
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-510	11
β-strand	517-520	4	14
α-helix	522-523	2
β-strand	534-536	3	14
β-strand	554-557	4	14
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-604	14	14
β-strand	618-633	16	14
β-strand	636-642	7	14
β-strand	653-658	6	14
α-helix	665-682	18
β-strand	686-691	6	14
β-strand	694-707	14	14
α-helix	709-715	7
α-helix	718-720	3
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
α-helix	793-813	21
α-helix	815-817	3
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	903-922	20
α-helix	925-927	3
α-helix	934-941	8
α-helix	943-950	8
α-helix	962-975	14
α-helix	983-994	12
α-helix	997-1003	7

Chain D: 13 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
β-strand	7-8	2	17
α-helix	12-14	3
β-strand	20-24	5	17
β-strand	27-31	5	17
α-helix	37-38	2
β-strand	45-51	7	17
β-strand	54-59	6	17
β-strand	61-62	2	18
α-helix	69-71	3
β-strand	73	1	19
β-strand	76-80	5	18
β-strand	90-94	5	18
β-strand	97	1	19
α-helix	102	1
β-strand	103	1	19
α-helix	104	1
β-strand	107-116	10	18
β-strand	119-127	9	18
α-helix	128	1
β-strand	130-131	2	20
α-helix	133-136	4
β-strand	138	1	21
β-strand	141-147	7	20
β-strand	150-156	7	20
β-strand	159-161	3	21
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	21
α-helix	178-179	2
β-strand	181-186	6	20
β-strand	191-196	6	20
β-strand	205	1	22
β-strand	208-212	5	23
β-strand	215-219	5	23
β-strand	222	1	22
β-strand	223	1	24
β-strand	228	1	24
β-strand	233-239	7	23
β-strand	246-252	7	23
β-strand	259	1	25
β-strand	262-266	5	26
β-strand	270-274	5	26
β-strand	277	1	25
β-strand	283	1	25
β-strand	287-291	5	26
β-strand	298-302	5	26
α-helix	303-305	3
α-helix	309-313	5
β-strand	318-321	4	16
β-strand	326-332	7	16
α-helix	333-334	2
β-strand	343-349	7	16

Chain N: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	20-30	11
α-helix	38-47	10
α-helix	98-100	3
α-helix	101-116	16
α-helix	122-135	14
α-helix	142-157	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A, C	protein	625	Mus musculus	P15919 (AlphaFold model)
V(D)J recombination-activating protein 2	B, D	protein	359	Mus musculus	P21784 (AlphaFold model)
High mobility group protein B1	N	protein	163	Homo sapiens	P09429 (AlphaFold model)
Nicked 12RSS intermediate reverse strand	F	DNA	40	Homo sapiens
DNA (5'-d(gpcpcptpgptpcptptpa)-3')	I	DNA	10	Homo sapiens
Nicked 12RSS intermediate forward strand	L	DNA	30	Homo sapiens
Intact 23RSS substrate reverse strand	G	DNA	56	Homo sapiens
Intact 23RSS substrate forward strand	J	DNA	56	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>6CIM_1 V(D)J recombination-activating protein 1 (chains A, C)
VHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARN
EHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHAL
RNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSAL
VSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFS
FTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMK
SSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVF
HSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAE
FYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETV
DAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTK
FKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYE
MEDVLKHHWLYTSKYLQKFMNAHNA

Sequence of entity 2 (B, D), FASTA

>6CIM_2 V(D)J recombination-activating protein 2 (chains B, D)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQ

Sequence of entity 3 (N), FASTA

>6CIM_3 High mobility group protein B1 (chains N)
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
EDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL
SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

Sequence of entity 4 (F), FASTA

>6CIM_4 Nicked 12RSS intermediate reverse strand (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGC

Sequence of entity 5 (I), FASTA

>6CIM_5 DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') (chains I)
GCCTGTCTTA

Sequence of entity 6 (L), FASTA

>6CIM_6 Nicked 12RSS intermediate forward strand (chains L)
CACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 7 (G), FASTA

>6CIM_7 Intact 23RSS substrate reverse strand (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGAT

Sequence of entity 8 (J), FASTA

>6CIM_8 Intact 23RSS substrate forward strand (chains J)
ATCTGGCCTGTCTTACACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCCG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MN	Manganese (II) ion	Mn	2

Primary citation

Cracking the DNA Code for V(D)J Recombination. Kim, M.S., Chuenchor, W., Chen, X. et al. Mol Cell (2018) 70:358-370.e4. DOI 10.1016/j.molcel.2018.03.008 · 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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