6OES: Mouse RAG1/2 STC complex

Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain). Determined by electron microscopy at 3.06 Å resolution. Released 22 Jan 2020.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: Mus musculus, Escherichia coli K-12
Chains: 10
Atoms: 16,829
Mol. weight: 422.5 kDa
Ligands: ZN, CA
Released: 22 Jan 2020

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

Secondary structure: helices and β-sheets

6OES contains 64 α-helices and 93 β-strands across 4 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: 26 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-506	7
β-strand	517-520	4	1
α-helix	522-523	2
β-strand	535-536	2	1
β-strand	554-556	3	1
α-helix	559-580	22
β-strand	590-602	13	1
α-helix	606-608	3
β-strand	619-632	14	1
β-strand	637-642	6	1
β-strand	653-658	6	1
α-helix	665-681	17
α-helix	682-684	3
β-strand	686-691	6	1
β-strand	694-706	13	1
α-helix	709-715	7
β-strand	725	1	2
β-strand	733	1	2
α-helix	734-740	7
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-811	19
α-helix	823-840	18
α-helix	852-857	6
α-helix	860-867	8
α-helix	874-889	16
α-helix	890-892	3
α-helix	903-907	5
α-helix	909-922	14
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
α-helix	1002-1004	3

Chain B: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	3
β-strand	7-8	2	4
α-helix	12-14	3
β-strand	20-24	5	4
β-strand	27-31	5	4
β-strand	46-51	6	4
β-strand	54-59	6	4
β-strand	62	1	5
β-strand	76-80	5	5
β-strand	90-94	5	5
β-strand	97	1	6
β-strand	103	1	6
β-strand	107-116	10	5
β-strand	119-127	9	5
α-helix	128	1
β-strand	130-131	2	7
α-helix	133-135	3
β-strand	138	1	8
β-strand	141-147	7	7
β-strand	150-156	7	7
β-strand	159-161	3	8
α-helix	169-171	3
β-strand	175-177	3	8
α-helix	178-179	2
β-strand	182-186	5	7
β-strand	191-195	5	7
β-strand	208-211	4	9
β-strand	215-219	5	9
β-strand	233-239	7	9
β-strand	246-252	7	9
β-strand	259	1	10
β-strand	262-267	6	11
β-strand	270-274	5	11
β-strand	277	1	10
β-strand	283	1	10
β-strand	288-291	4	11
β-strand	298-301	4	11
α-helix	303-305	3
β-strand	318-321	4	3
β-strand	326-332	7	3
β-strand	343-349	7	3

Chain C: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-507	8
β-strand	518-519	2	12
α-helix	522-523	2
β-strand	535-536	2	12
β-strand	555-556	2	12
α-helix	559-568	10
α-helix	571-580	10
β-strand	590-603	14	12
β-strand	618-624	7	12
β-strand	626-633	8	12
β-strand	636-642	7	12
β-strand	653-658	6	12
α-helix	665-682	18
β-strand	687-691	5	12
β-strand	694-706	13	12
α-helix	709-715	7
β-strand	725	1	13
β-strand	733	1	13
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-839	17
α-helix	843-845	3
α-helix	851-857	7
α-helix	860-866	7
α-helix	873-894	22
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	959-974	16
α-helix	983-994	12
α-helix	997-1000	4
α-helix	1002-1004	3

Chain D: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
β-strand	7-8	2	15
α-helix	12-14	3
β-strand	20-24	5	15
β-strand	27-31	5	15
β-strand	46-51	6	15
β-strand	54-59	6	15
β-strand	62	1	16
β-strand	76-80	5	16
β-strand	90-94	5	16
β-strand	97	1	17
β-strand	103	1	17
β-strand	107-116	10	16
β-strand	119-127	9	16
α-helix	128	1
β-strand	130-131	2	18
α-helix	133-135	3
β-strand	138	1	19
β-strand	141-147	7	18
β-strand	150-156	7	18
β-strand	159-161	3	19
α-helix	169-171	3
β-strand	175-177	3	19
α-helix	178-179	2
β-strand	182-186	5	18
β-strand	191-195	5	18
β-strand	208-211	4	20
β-strand	215-219	5	20
β-strand	233-239	7	20
β-strand	246-252	7	20
β-strand	259	1	21
β-strand	262-267	6	22
β-strand	270-274	5	22
β-strand	277	1	21
β-strand	283	1	21
β-strand	288-291	4	22
β-strand	298-301	4	22
α-helix	303-305	3
β-strand	318-321	4	14
β-strand	326-332	7	14
β-strand	343-349	7	14

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 (35-mer)	F	DNA	50	Escherichia coli K-12
DNA (5'-d(cpcptpgpgpaptpcptpgpgpcpcptp*g)-3')	I, J	DNA	15	Escherichia coli K-12
DNA (34-mer)	G	DNA	61	Escherichia coli K-12
DNA (5'-d(pcpapcpapgptpgpaptpapcpapgpcp*c)-3')	L	DNA	30	Escherichia coli K-12
DNA (5'-d(pcpapcpapgptpgpaptpgpcpapapa)-3')	M	DNA	41	Escherichia coli K-12

Sequence of entity 1 (A, C), FASTA

>6OES_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

>6OES_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

>6OES_3 DNA (35-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGCGGCGCAGGCCAGATCCAGG

Sequence of entity 4 (I, J), FASTA

>6OES_4 DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3') (chains I, J)
CCTGGATCTGGCCTG

Sequence of entity 5 (G), FASTA

>6OES_5 DNA (34-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGCGCCGCAGGCCAGATCCAG
G

Sequence of entity 6 (L), FASTA

>6OES_6 DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3') (chains L)
CACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 7 (M), FASTA

>6OES_7 DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3') (chains M)
CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCCG

Ligands and cofactors

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

Primary citation

How mouse RAG recombinase avoids DNA transposition. Chen, X., Cui, Y., Wang, H. et al. Nat Struct Mol Biol (2020) 27:127-133. DOI 10.1038/s41594-019-0366-z · 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
9LQV 3.1 Å, Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)

Browse structure collections

About this viewer

MolViewer shows 6OES 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.