6OEM: Mouse RAG1/2 PRC complex

Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0). Determined by electron microscopy at 3.6 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Mus musculus, Escherichia coli K-12, Homo sapiens
Chains: 10
Atoms: 19,707
Mol. weight: 458.53 kDa
Ligands: ZN, MG
Released: 29 Jan 2020

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

Secondary structure: helices and β-sheets

6OEM contains 72 α-helices and 101 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	401-422	22
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-473	10
α-helix	479-492	14
α-helix	500-510	11
β-strand	517-519	3	1
β-strand	535-536	2	1
β-strand	554-556	3	1
α-helix	559-569	11
α-helix	571-580	10
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	934-940	7
α-helix	943-949	7
α-helix	962-964	3
α-helix	966-974	9
α-helix	982-994	13
α-helix	997-1003	7
α-helix	1004-1006	3

Chain B: 5 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	3
β-strand	7	1	4
β-strand	20-24	5	5
β-strand	27-31	5	5
β-strand	46-47	2	5
β-strand	50-51	2	4
β-strand	54-55	2	4
β-strand	58-59	2	5
β-strand	62	1	6
β-strand	75-80	6	7
β-strand	90-95	6	7
β-strand	98	1	8
β-strand	102	1	8
β-strand	107-110	4	7
β-strand	112-116	5	6
β-strand	119-122	4	6
β-strand	125-127	3	7
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
α-helix	162-163	2
β-strand	175-177	3	10
β-strand	181-186	6	9
β-strand	191-196	6	9
β-strand	205	1	11
β-strand	208-211	4	12
β-strand	215-219	5	12
β-strand	222	1	11
β-strand	223	1	13
β-strand	228	1	13
β-strand	233-239	7	12
β-strand	246-252	7	12
β-strand	259	1	14
β-strand	263-267	5	15
β-strand	270-273	4	15
β-strand	277	1	14
α-helix	283-284	2
β-strand	288-292	5	15
β-strand	297-301	5	15
α-helix	309-313	5
β-strand	318-321	4	3
β-strand	326-332	7	3
α-helix	333-334	2
β-strand	343-349	7	3

Chain C: 28 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	396-398	3
α-helix	401-418	18
α-helix	419-423	5
α-helix	427-440	14
α-helix	445-456	12
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-508	9
β-strand	518-519	2	2
β-strand	535-536	2	2
β-strand	555-556	2	2
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-598	8	2
β-strand	601-604	4	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	709-712	4
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-775	7
α-helix	793-812	20
α-helix	823-840	18
α-helix	851-857	7
α-helix	860-867	8
α-helix	873-893	21
α-helix	903-906	4
α-helix	909-922	14
α-helix	934-940	7
α-helix	943-949	7
α-helix	964-973	10
α-helix	982-994	13
α-helix	997-1003	7
α-helix	1004-1007	4

Chain D: 6 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	16
β-strand	7	1	17
β-strand	20-24	5	18
β-strand	27-31	5	18
β-strand	46-47	2	18
β-strand	50-51	2	17
β-strand	54-55	2	17
β-strand	58-59	2	18
β-strand	62	1	19
β-strand	75-80	6	20
β-strand	90-95	6	20
β-strand	98	1	21
β-strand	102	1	21
β-strand	107-111	5	20
β-strand	112-116	5	19
β-strand	119-122	4	19
β-strand	125-127	3	20
β-strand	130-131	2	22
α-helix	133-136	4
β-strand	138	1	23
β-strand	141-147	7	22
β-strand	150-156	7	22
β-strand	159-161	3	23
α-helix	162-163	2
β-strand	175-177	3	23
β-strand	181-186	6	22
β-strand	191-196	6	22
β-strand	205	1	24
β-strand	208-211	4	25
β-strand	215-219	5	25
β-strand	222	1	24
β-strand	223	1	26
β-strand	228	1	26
β-strand	233-239	7	25
β-strand	246-252	7	25
β-strand	263-267	5	27
β-strand	270-273	4	27
α-helix	274-275	2
α-helix	283-284	2
β-strand	288-292	5	27
β-strand	297-301	5	27
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 H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	102-116	15
α-helix	122-135	14
α-helix	138-141	4
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	141	Homo sapiens	P09429 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OEM_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

>6OEM_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

>6OEM_3 DNA (57-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGATCCAG
G

Sequence of entity 4 (I), FASTA

>6OEM_4 DNA (46-MER) (chains I)
CCTGGATCTGGCCTGTCTTACACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 5 (F), FASTA

>6OEM_5 DNA (46-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGATCCAGG

Sequence of entity 6 (J), FASTA

>6OEM_6 DNA (57-MER) (chains J)
CCTGGATCTGGCCTGTCTTACACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCC
G

Sequence of entity 7 (H, N), FASTA

>6OEM_7 High mobility group protein B1 (chains H, N)
SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYERE
MKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN
NTAADDKQPYEKKAAKLKEKY

Ligands and cofactors

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