6OEO: Mouse RAG1/2 NFC complex

Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1). Determined by electron microscopy at 3.69 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 3.69 Å
Organisms: Mus musculus, Escherichia coli K-12, Homo sapiens
Chains: 9
Atoms: 19,516
Mol. weight: 444.65 kDa
Ligands: ZN, CA
Released: 29 Jan 2020

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

Secondary structure: helices and β-sheets

6OEO contains 68 α-helices and 94 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: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	402-407	6
α-helix	409-421	13
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-473	10
α-helix	480-492	13
α-helix	501-507	7
β-strand	518-520	3	1
α-helix	522-523	2
β-strand	535-536	2	1
β-strand	554-556	3	1
α-helix	560-569	10
α-helix	571-580	10
β-strand	590-599	10	1
β-strand	620-633	14	1
β-strand	636-642	7	1
β-strand	653-658	6	1
α-helix	665-681	17
β-strand	686-690	5	1
β-strand	695-707	13	1
α-helix	709-715	7
β-strand	718	1	2
β-strand	725	1	3
β-strand	733	1	3
α-helix	734-737	4
α-helix	750-762	13
α-helix	769-775	7
β-strand	779	1	2
α-helix	794-812	19
α-helix	825-840	16
α-helix	851-857	7
α-helix	860-869	10
α-helix	874-889	16
α-helix	891-894	4
α-helix	905-922	18
α-helix	935-941	7
α-helix	943-950	8
α-helix	959-972	14
α-helix	985-994	10
α-helix	1000-1003	4

Chain B: 5 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	7	1	5
α-helix	12-14	3
β-strand	20-24	5	5
β-strand	27-31	5	5
β-strand	45-51	7	5
β-strand	54-59	6	5
β-strand	76-81	6	6
β-strand	89-94	6	6
β-strand	107-112	6	6
β-strand	116	1	7
β-strand	119	1	7
β-strand	122-127	6	6
β-strand	130-131	2	8
α-helix	133-136	4
β-strand	138	1	9
β-strand	141-147	7	8
β-strand	150-156	7	8
β-strand	159-161	3	9
α-helix	162-163	2
β-strand	175-177	3	9
α-helix	178-179	2
β-strand	182-186	5	8
β-strand	191-195	5	8
β-strand	205	1	10
β-strand	208-212	5	11
β-strand	215-219	5	11
β-strand	222	1	10
β-strand	223	1	12
β-strand	228	1	12
β-strand	234-239	6	11
β-strand	246-251	6	11
β-strand	259	1	13
β-strand	263-267	5	14
β-strand	270-273	4	14
β-strand	277-279	3	13
β-strand	282-283	2	13
β-strand	288-291	4	14
β-strand	298-301	4	14
α-helix	309-313	5
β-strand	318-321	4	4
β-strand	326-331	6	4
β-strand	344-349	6	4

Chain C: 27 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	403-422	20
α-helix	428-440	13
α-helix	445-454	10
α-helix	464-473	10
α-helix	479-492	14
α-helix	501-507	7
β-strand	518-520	3	15
α-helix	522-523	2
β-strand	535-536	2	15
β-strand	554-556	3	15
α-helix	559-568	10
α-helix	571-580	10
β-strand	591-601	11	15
β-strand	620-633	14	15
β-strand	636-642	7	15
β-strand	653-658	6	15
α-helix	665-681	17
β-strand	686-690	5	15
β-strand	695-704	10	15
α-helix	709-714	6
β-strand	725	1	16
β-strand	733	1	16
α-helix	734-739	6
α-helix	751-762	12
α-helix	769-776	8
α-helix	793-813	21
α-helix	825-841	17
α-helix	851-857	7
α-helix	860-867	8
α-helix	873-894	22
α-helix	903-922	20
α-helix	934-941	8
α-helix	943-950	8
α-helix	954-956	3
α-helix	959-962	4
α-helix	964-974	11
α-helix	985-994	10
α-helix	1000-1003	4

Chain D: 6 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
α-helix	12-14	3
β-strand	20-24	5	18
β-strand	27-31	5	18
β-strand	46-51	6	18
β-strand	54-58	5	18
β-strand	62	1	19
β-strand	76-80	5	19
β-strand	90-94	5	19
β-strand	107-116	10	19
β-strand	119-127	9	19
β-strand	130	1	20
α-helix	133-135	3
β-strand	138	1	21
β-strand	141-147	7	20
β-strand	150-156	7	20
β-strand	159-160	2	21
α-helix	161-163	3
β-strand	176-177	2	21
α-helix	178-179	2
β-strand	182-186	5	20
β-strand	191-195	5	20
β-strand	207-212	6	22
β-strand	215-220	6	22
β-strand	233-239	7	22
β-strand	246-252	7	22
β-strand	259	1	23
β-strand	262-267	6	24
β-strand	270-274	5	24
β-strand	277	1	23
β-strand	283	1	23
β-strand	288-292	5	24
β-strand	297-301	5	24
α-helix	309-312	4
β-strand	318-321	4	17
β-strand	326-332	7	17
α-helix	335-337	3
β-strand	343-349	7	17

Chain N: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	102-116	15
α-helix	122-134	13
α-helix	142-154	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 (46-mer)	F	DNA	50	Escherichia coli K-12
DNA (46-mer)	I	DNA	50	Escherichia coli K-12
DNA (57-mer)	G	DNA	61	Escherichia coli K-12
DNA (57-mer)	J	DNA	61	Escherichia coli K-12
High mobility group protein B1	N	protein	163	Homo sapiens	P09429 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OEO_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

>6OEO_2 V(D)J recombination-activating protein 2 (chains B, D)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQK
IVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCC
PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNE
HVQIARALQTPKRNPPLQKPPMKSLHKKGSGKVLTPAKKSFLRRLFD

Sequence of entity 3 (F), FASTA

>6OEO_3 DNA (46-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGATCCAGG

Sequence of entity 4 (I), FASTA

>6OEO_4 DNA (46-MER) (chains I)
CCTGGATCTGGCCTGTCTTACACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 5 (G), FASTA

>6OEO_5 DNA (57-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGATCCAG
G

Sequence of entity 6 (J), FASTA

>6OEO_6 DNA (57-MER) (chains J)
CCTGGATCTGGCCTGTCTTACACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCC
G

Sequence of entity 7 (N), FASTA

>6OEO_7 High mobility group protein B1 (chains N)
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
EDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL
SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	4

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)

Browse structure collections

About this viewer

MolViewer shows 6OEO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.