6OEN: Mouse RAG1/2 PRC complex

Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1). Determined by electron microscopy at 4.3 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 4.3 Å
Organisms: Mus musculus, Escherichia coli K-12, Homo sapiens
Chains: 10
Atoms: 19,649
Mol. weight: 463.43 kDa
Ligands: CA, ZN
Released: 29 Jan 2020

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

Secondary structure: helices and β-sheets

6OEN contains 69 α-helices and 100 β-strands across 6 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	401-407	7
α-helix	409-422	14
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-474	11
α-helix	478-492	15
α-helix	500-510	11
β-strand	518-519	2	1
β-strand	535-536	2	1
β-strand	554-556	3	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	687-690	4	1
β-strand	695-706	12	1
α-helix	709-715	7
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-811	19
α-helix	823-840	18
α-helix	851-857	7
α-helix	860-867	8
α-helix	875-893	19
α-helix	903-906	4
α-helix	909-922	14
α-helix	934-941	8
α-helix	943-950	8
α-helix	963-974	12
α-helix	982-994	13
α-helix	997-1003	7

Chains B and D: 4 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	4
β-strand	7	1	5
α-helix	12-14	3
β-strand	20-24	5	6
β-strand	27-31	5	6
β-strand	46-50	5	6
β-strand	54	1	5
β-strand	55-59	5	6
β-strand	61-62	2	7
β-strand	75-80	6	8
β-strand	90-95	6	8
β-strand	107-110	4	8
β-strand	112-116	5	7
β-strand	119-122	4	7
β-strand	125-127	3	8
β-strand	130-131	2	9
α-helix	133-136	4
β-strand	138	1	10
β-strand	141-147	7	9
β-strand	150-156	7	9
β-strand	159-161	3	10
β-strand	175-177	3	10
β-strand	181-185	5	9
β-strand	191-196	6	9
β-strand	205	1	11
β-strand	208-212	5	12
β-strand	215-219	5	12
β-strand	222	1	11
β-strand	223	1	13
β-strand	228	1	13
β-strand	234-239	6	12
β-strand	246-250	5	12
β-strand	259	1	14
β-strand	263-267	5	15
β-strand	270-273	4	15
β-strand	277	1	14
β-strand	283	1	14
β-strand	288-292	5	15
β-strand	297-301	5	15
α-helix	305-308	4
α-helix	309-312	4
β-strand	320-321	2	4
β-strand	326-332	7	4
β-strand	343-349	7	4

Chain C: 29 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	401-418	18
α-helix	419-423	5
α-helix	427-440	14
α-helix	445-456	12
α-helix	464-474	11
α-helix	478-492	15
α-helix	500-508	9
β-strand	518-519	2	2
β-strand	534-536	3	2
α-helix	548-549	2
β-strand	554-557	4	2
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-604	14	2
β-strand	618-633	16	2
β-strand	636-642	7	2
β-strand	653-658	6	2
α-helix	665-682	18
β-strand	687-689	3	2
β-strand	696-706	11	2
α-helix	709-715	7
β-strand	725	1	3
β-strand	733	1	3
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-775	7
α-helix	793-813	21
α-helix	823-840	18
α-helix	851-857	7
α-helix	860-867	8
α-helix	874-893	20
α-helix	903-906	4
α-helix	909-918	10
α-helix	919-923	5
α-helix	934-940	7
α-helix	944-949	6
α-helix	964-974	11
α-helix	982-994	13
α-helix	997-1003	7
α-helix	1005-1007	3

Chain H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	102-116	15
α-helix	122-135	14
α-helix	142-154	13

Chain N: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	101-116	16
α-helix	123-135	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A, C	protein	1040	Mus musculus	P15919 (AlphaFold model)
V(D)J recombination-activating protein 2	B, D	protein	527	Mus musculus	P21784 (AlphaFold model)
DNA (57-mer)	G	DNA	61	Escherichia coli K-12
DNA (46-mer)	I	DNA	50	Escherichia coli K-12
DNA (46-mer)	F	DNA	50	Escherichia coli K-12
DNA (57-mer)	J	DNA	61	Escherichia coli K-12
High mobility group protein B1	H, N	protein	163	Homo sapiens	P09429 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OEN_1 V(D)J recombination-activating protein 1 (chains A, C)
MAASLPSTLSFSSAPDEIQHPQIKFSEWKFKLFRVRSFEKAPEEAQKEKDSSEGKPYLEQ
SPVVPEKPGGQNSILTQRALKLHPKFSKKFHADGKSSDKAVHQARLRHFCRICGNRFKSD
GHSRRYPVHGPVDAKTQSLFRKKEKRVTSWPDLIARIFRIDVKADVDSIHPTEFCHDCWS
IMHRKFSSSHSQVYFPRKVTVEWHPHTPSCDICFTAHRGLKRKRHQPNVQLSKKLKTVLN
HARRDRRKRTQARVSSKEVLKKISNCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADP
VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDC
NEEVSLEKYNHHVSSHKESKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFAD
KEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQ
YHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSG
LASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCD
GMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLA
DESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEA
SGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVS
AKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKR
MNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAK
ECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEG
NQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNALKSSGFTMNSKE
TLGDPLGIEDSLESQDSMEF

Sequence of entity 2 (B, D), FASTA

>6OEN_2 V(D)J recombination-activating protein 2 (chains B, D)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQK
IVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCC
PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNE
HVQIARALQTPKRNPPLQKPPMKSLHKKGSGKVLTPAKKSFLRRLFD

Sequence of entity 3 (G), FASTA

>6OEN_3 DNA (57-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGATCCAG
G

Sequence of entity 4 (I), FASTA

>6OEN_4 DNA (46-MER) (chains I)
CCTGGATCTGGCCTGTCTTACACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 5 (F), FASTA

>6OEN_5 DNA (46-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGATCCAGG

Sequence of entity 6 (J), FASTA

>6OEN_6 DNA (57-MER) (chains J)
CCTGGATCTGGCCTGTCTTACACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCC
G

Sequence of entity 7 (H, N), FASTA

>6OEN_7 High mobility group protein B1 (chains H, N)
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
EDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL
SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
ZN	Zinc ion	Zn	2

Primary citation

Cutting antiparallel DNA strands in a single active site. Chen, X., Cui, Y., Best, R.B. et al. Nat Struct Mol Biol (2020) 27:119-126. DOI 10.1038/s41594-019-0363-2 · 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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