6OET: Mouse RAG1/2 STC complex

Cryo-EM structure of mouse RAG1/2 STC complex. Determined by electron microscopy at 3.4 Å resolution. Released 22 Jan 2020.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Mus musculus, Escherichia coli K-12
Chains: 10
Atoms: 19,604
Mol. weight: 422.5 kDa
Ligands: ZN, CA
Released: 22 Jan 2020

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

Secondary structure: helices and β-sheets

6OET contains 73 α-helices and 95 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: 29 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	405-422	18
α-helix	428-441	14
α-helix	445-455	11
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-505	6
β-strand	517-519	3	1
α-helix	522-523	2
β-strand	535-536	2	1
β-strand	554-556	3	1
α-helix	559-569	11
α-helix	571-580	10
β-strand	590-602	13	1
β-strand	619-633	15	1
β-strand	636-642	7	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
β-strand	725	1	2
β-strand	733	1	2
α-helix	736-738	3
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-811	19
α-helix	823-841	19
α-helix	843-845	3
α-helix	852-857	6
α-helix	861-867	7
α-helix	874-889	16
α-helix	890-892	3
α-helix	903-907	5
α-helix	909-923	15
α-helix	934-941	8
α-helix	943-950	8
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-999	3
α-helix	1005-1007	3

Chains B and D: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	7-8	2	4
α-helix	12-14	3
β-strand	15-24	10	4
β-strand	27-33	7	4
α-helix	37-38	2
β-strand	46-51	6	4
β-strand	54-59	6	4
β-strand	61-62	2	5
β-strand	76-79	4	5
β-strand	91-94	4	5
β-strand	97	1	6
β-strand	103	1	6
β-strand	107-116	10	5
β-strand	119-127	9	5
β-strand	130-131	2	7
α-helix	133-136	4
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
β-strand	182-186	5	7
β-strand	191-195	5	7
β-strand	205-210	6	9
β-strand	215-216	2	10
β-strand	217-222	6	9
β-strand	223	1	11
β-strand	228	1	11
β-strand	233	1	9
β-strand	234-239	6	10
β-strand	246-251	6	10
β-strand	262-265	4	12
β-strand	270-274	5	12
β-strand	288-291	4	12
β-strand	298-301	4	12
α-helix	303-305	3
α-helix	309-312	4
β-strand	318-321	4	3
β-strand	326-332	7	3
β-strand	343-349	7	3

Chain C: 32 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	396-398	3
α-helix	401-407	7
α-helix	411-422	12
α-helix	427-441	15
α-helix	445-455	11
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-507	8
β-strand	517-519	3	13
α-helix	522-523	2
β-strand	534-536	3	13
β-strand	554-557	4	13
α-helix	559-569	11
α-helix	571-579	9
β-strand	590-602	13	13
α-helix	606-608	3
β-strand	619-632	14	13
β-strand	637-642	6	13
β-strand	653-658	6	13
α-helix	666-682	17
β-strand	687-690	4	13
β-strand	695-699	5	13
β-strand	702-706	5	13
α-helix	709-715	7
β-strand	725	1	14
β-strand	733	1	14
α-helix	734-739	6
α-helix	751-762	12
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-841	19
α-helix	843-845	3
α-helix	851-857	7
α-helix	860-866	7
α-helix	873-894	22
α-helix	903-906	4
α-helix	909-922	14
α-helix	934-941	8
α-helix	943-949	7
α-helix	959-973	15
α-helix	984-994	11
α-helix	997-1000	4
α-helix	1001-1003	3

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 (50-mer)	F	DNA	50	Escherichia coli K-12
DNA (5'-d(cpcptpgpgpaptpcptpgpgpcpcptp*g)-3')	I, J	DNA	15	Escherichia coli K-12
DNA (59-mer)	G	DNA	61	Escherichia coli K-12
DNA (30-mer)	L	DNA	30	Escherichia coli K-12
DNA (39-mer)	M	DNA	41	Escherichia coli K-12

Sequence of entity 1 (A, C), FASTA

>6OET_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

>6OET_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

>6OET_3 DNA (50-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGCGGCGCAGGCCAGATCCAGG

Sequence of entity 4 (I, J), FASTA

>6OET_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

>6OET_5 DNA (59-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGCGCCGCAGGCCAGATCCAG
G

Sequence of entity 6 (L), FASTA

>6OET_6 DNA (30-MER) (chains L)
CACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 7 (M), FASTA

>6OET_7 DNA (39-MER) (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
6OES 3.06 Å, Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)

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