6CIJ: VJ recombination-activating protein 1

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A). Determined by electron microscopy at 3.9 Å resolution. Released 25 Apr 2018.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Mus musculus, Homo sapiens
Chains: 11
Atoms: 20,413
Mol. weight: 378.61 kDa
Ligands: CA, ZN
Released: 25 Apr 2018

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

Secondary structure: helices and β-sheets

6CIJ contains 84 α-helices and 113 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: 32 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	404-422	19
α-helix	427-441	15
α-helix	445-454	10
α-helix	461-463	3
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-510	11
β-strand	518-519	2	1
α-helix	522-523	2
β-strand	535-536	2	1
α-helix	548-549	2
β-strand	554-556	3	1
α-helix	559-569	11
α-helix	571-580	10
β-strand	590-601	12	1
α-helix	605-607	3
β-strand	620-633	14	1
β-strand	636-642	7	1
α-helix	649-651	3
β-strand	653-658	6	1
α-helix	665-682	18
β-strand	687-688	2	1
β-strand	690-691	2	2
β-strand	694-695	2	2
β-strand	697-706	10	1
α-helix	709-715	7
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-841	19
α-helix	852-857	6
α-helix	860-867	8
α-helix	874-889	16
α-helix	890-893	4
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-923	15
α-helix	934-941	8
α-helix	943-950	8
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1000	4

Chain B: 5 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	19
β-strand	7	1	20
α-helix	12-14	3
β-strand	22-24	3	20
β-strand	27-30	4	20
β-strand	46-51	6	20
β-strand	54-59	6	20
β-strand	62	1	21
α-helix	69-71	3
β-strand	78	1	22
β-strand	90	1	23
β-strand	92	1	22
β-strand	93-94	2	24
β-strand	97	1	25
β-strand	103	1	25
β-strand	107-109	3	24
β-strand	111	1	23
β-strand	112-115	4	21
β-strand	120-122	3	21
β-strand	125-127	3	24
β-strand	130-131	2	26
α-helix	133-136	4
β-strand	138	1	27
β-strand	141-146	6	26
β-strand	151-156	6	26
β-strand	159-161	3	27
β-strand	175-177	3	27
α-helix	178-179	2
β-strand	182-186	5	26
β-strand	191-195	5	26
β-strand	205	1	28
β-strand	208-211	4	29
β-strand	215-219	5	29
β-strand	222	1	28
β-strand	223	1	30
β-strand	228	1	30
β-strand	233-237	5	29
β-strand	239	1	31
β-strand	246	1	31
β-strand	251	1	29
β-strand	262-267	6	32
β-strand	270-274	5	32
β-strand	277	1	33
β-strand	283	1	33
β-strand	288-289	2	32
β-strand	292	1	34
β-strand	297	1	34
β-strand	300	1	32
α-helix	309-312	4
β-strand	318-321	4	19
β-strand	326-332	7	19
β-strand	343-349	7	19

Chain C: 31 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	401-420	20
α-helix	427-440	14
α-helix	445-456	12
α-helix	464-473	10
α-helix	478-491	14
α-helix	500-506	7
α-helix	507-509	3
β-strand	518-519	2	3
β-strand	535-536	2	3
β-strand	554-556	3	3
α-helix	559-569	11
α-helix	571-580	10
β-strand	590-603	14	3
α-helix	606-608	3
β-strand	618-633	16	3
β-strand	636-642	7	3
α-helix	649-651	3
β-strand	653-658	6	3
α-helix	665-682	18
β-strand	687-691	5	3
β-strand	694-706	13	3
α-helix	709-715	7
β-strand	718	1	4
α-helix	736-738	3
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	4
α-helix	793-812	20
α-helix	823-840	18
α-helix	851-857	7
α-helix	860-866	7
α-helix	867-869	3
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-922	14
α-helix	934-941	8
α-helix	943-949	7
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-995	13
α-helix	997-1001	5

Chain D: 7 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	7	1	6
β-strand	22-24	3	7
β-strand	27-30	4	7
β-strand	46-47	2	7
β-strand	49-51	3	6
β-strand	54-56	3	6
β-strand	61-62	2	8
α-helix	69-72	4
β-strand	75-78	4	9
β-strand	91-95	5	9
β-strand	97	1	10
β-strand	103	1	10
β-strand	107-110	4	9
β-strand	114-115	2	8
β-strand	120-122	3	8
β-strand	125-127	3	9
β-strand	130-131	2	11
α-helix	133-136	4
β-strand	138	1	12
β-strand	141-146	6	11
β-strand	151-156	6	11
β-strand	159-161	3	12
α-helix	169-171	3
β-strand	175-177	3	12
α-helix	178-179	2
β-strand	182-185	4	11
β-strand	191-195	5	11
β-strand	205	1	13
β-strand	208-210	3	14
β-strand	215-219	5	14
β-strand	222	1	13
β-strand	223	1	15
β-strand	228	1	15
β-strand	233-237	5	14
β-strand	238-239	2	16
β-strand	246-247	2	16
β-strand	250-252	3	14
β-strand	259	1	17
β-strand	263-267	5	18
β-strand	270-273	4	18
β-strand	277	1	17
α-helix	282	1
β-strand	283	1	17
α-helix	284	1
β-strand	288-291	4	18
β-strand	301	1	18
α-helix	311-313	3
β-strand	318-321	4	5
β-strand	326-332	7	5
β-strand	343-349	7	5

Chain N: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	17-29	13
α-helix	39-42	4
α-helix	45-48	4
α-helix	58-65	8
α-helix	68-71	4
α-helix	101-116	16
α-helix	122-133	12
α-helix	142-146	5
α-helix	147-157	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A, C	protein	776	Mus musculus	P15919 (AlphaFold model)
DNA (46-mer)	F	DNA	46	Homo sapiens
DNA (5'-d(gpaptpcptpgpgpcpcptpgptpcptptpa)-3')	I	DNA	16	Homo sapiens
DNA (5'-d(pcptpgpgpaptpcptpgpgpcpcptpgptpcptptp*a)-3')	J	DNA	20	Homo sapiens
DNA (60-mer)	G	DNA	61	Homo sapiens
High mobility group protein B1	N	protein	163	Homo sapiens	P09429 (AlphaFold model)
DNA (30-mer)	L	DNA	30	Homo sapiens
V(D)J recombination-activating protein 2	B, D	protein	520	Mus musculus	P21784 (AlphaFold model)
DNA (41-mer)	M	DNA	41	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>6CIJ_1 V(D)J recombination-activating protein 1 (chains A, C)
NCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY
CPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKESKETLV
HINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNE
HRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALR
NAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALV
SALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSF
TVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKS
SELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFH
SITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEF
YKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVD
AVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKF
KYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEM
EDVLKHHWLYTSKYLQKFMNAHNALKSSGFTMNSKETLGDPLGIEDSLESQDSMEF

Sequence of entity 2 (F), FASTA

>6CIJ_2 DNA (46-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGATC

Sequence of entity 3 (I), FASTA

>6CIJ_3 DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') (chains I)
GATCTGGCCTGTCTTA

Sequence of entity 4 (J), FASTA

>6CIJ_4 DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') (chains J)
CCTGGATCTGGCCTGTCTTA

Sequence of entity 5 (G), FASTA

>6CIJ_5 DNA (60-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGATCCAG
G

Sequence of entity 6 (N), FASTA

>6CIJ_6 High mobility group protein B1 (chains N)
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
EDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL
SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

Sequence of entity 7 (L), FASTA

>6CIJ_7 DNA (30-MER) (chains L)
CACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 8 (B, D), FASTA

>6CIJ_8 V(D)J recombination-activating protein 2 (chains B, D)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQK
IVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCC
PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNE
HVQIARALQAPKRNPPLQKPPMKSLHKKGSGKVLTPAKKS

Sequence of entity 9 (M), FASTA

>6CIJ_9 DNA (41-MER) (chains M)
CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCCG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	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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