6OER: Mouse RAG1/2 NFC complex

Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2). Determined by electron microscopy at 3.29 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Mus musculus, Escherichia coli K-12, Equus caballus
Chains: 9
Atoms: 19,482
Mol. weight: 444.6 kDa
Ligands: ZN, CA
Released: 29 Jan 2020

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

Secondary structure: helices and β-sheets

6OER contains 68 α-helices and 101 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	402-423	22
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-472	9
α-helix	478-492	15
α-helix	500-507	8
β-strand	518-519	2	1
α-helix	522-523	2
β-strand	534-536	3	1
β-strand	554-557	4	1
α-helix	559-567	9
α-helix	571-580	10
β-strand	590-600	11	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	687-690	4	1
β-strand	695-706	12	1
α-helix	709-716	8
β-strand	718	1	2
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
β-strand	779	1	2
α-helix	794-812	19
α-helix	825-841	17
α-helix	851-857	7
α-helix	860-866	7
α-helix	867-869	3
α-helix	875-894	20
α-helix	898-900	3
α-helix	903-923	21
α-helix	935-941	7
α-helix	943-950	8
α-helix	959-974	16
α-helix	982-995	14
α-helix	1000-1003	4

Chain B: 5 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	7-8	2	5
β-strand	20-24	5	5
β-strand	27-31	5	5
β-strand	46-51	6	5
β-strand	54-59	6	5
α-helix	68-70	3
β-strand	76-79	4	6
β-strand	91-94	4	6
β-strand	97-98	2	7
β-strand	102-103	2	7
β-strand	107-115	9	6
β-strand	120-127	8	6
β-strand	130-131	2	8
α-helix	133-135	3
β-strand	141-147	7	8
β-strand	150-156	7	8
β-strand	159-161	3	9
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	233-239	7	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	305-307	3
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: 28 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	401-407	7
α-helix	409-422	14
α-helix	428-440	13
α-helix	445-455	11
α-helix	464-473	10
α-helix	478-492	15
α-helix	501-508	8
β-strand	517-520	4	15
α-helix	522-523	2
β-strand	534-536	3	16
β-strand	554-557	4	16
α-helix	559-568	10
α-helix	571-580	10
β-strand	590-595	6	15
β-strand	598-602	5	16
β-strand	619-624	6	16
β-strand	626-631	6	15
β-strand	638-642	5	15
β-strand	653-658	6	16
α-helix	665-682	18
β-strand	686-690	5	15
β-strand	695-702	8	15
α-helix	709-715	7
β-strand	718	1	17
β-strand	725	1	18
β-strand	733	1	18
α-helix	736-739	4
α-helix	751-762	12
α-helix	769-776	8
β-strand	779	1	17
α-helix	793-812	20
α-helix	825-840	16
α-helix	851-857	7
α-helix	860-866	7
α-helix	867-869	3
α-helix	874-894	21
α-helix	903-922	20
α-helix	934-941	8
α-helix	943-950	8
α-helix	959-963	5
α-helix	965-974	10
α-helix	982-994	13
α-helix	1000-1003	4

Chain D: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	19
β-strand	7-8	2	20
α-helix	12-14	3
β-strand	20-24	5	20
β-strand	27-31	5	20
β-strand	46-51	6	20
β-strand	54-58	5	20
β-strand	76-80	5	21
β-strand	90-94	5	21
β-strand	97-98	2	22
β-strand	102-103	2	22
β-strand	107-116	10	21
β-strand	119-127	9	21
β-strand	130-131	2	23
α-helix	133-135	3
β-strand	141-147	7	23
β-strand	150-156	7	23
β-strand	159-161	3	24
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	24
β-strand	182-186	5	23
β-strand	191-195	5	23
β-strand	205	1	25
β-strand	208-212	5	26
β-strand	215-219	5	26
β-strand	222	1	25
β-strand	223	1	27
β-strand	228	1	27
β-strand	233-239	7	26
β-strand	246-252	7	26
β-strand	262-267	6	28
β-strand	270-274	5	28
β-strand	277	1	29
β-strand	283	1	29
β-strand	288-291	4	28
β-strand	298-301	4	28
α-helix	309-312	4
β-strand	318-321	4	19
β-strand	326-332	7	19
β-strand	343-349	7	19

Chain H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	103-106	4
α-helix	111-114	4
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 (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	H	protein	163	Equus caballus	Q08IE6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OER_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

>6OER_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

>6OER_3 DNA (46-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTTTAAGACAGGCCAGATCCAGG

Sequence of entity 4 (I), FASTA

>6OER_4 DNA (46-MER) (chains I)
CCTGGATCTGGCCTGTCTTACACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 5 (G), FASTA

>6OER_5 DNA (57-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTTTAAGACAGGCCAGATCCAG
G

Sequence of entity 6 (J), FASTA

>6OER_6 DNA (57-MER) (chains J)
CCTGGATCTGGCCTGTCTTACACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCC
G

Sequence of entity 7 (H), FASTA

>6OER_7 High mobility group protein B1 (chains H)
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 6OER 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.