6CG0: Mouse RAG1/2 HFC complex

Name: PDB 6CG0: Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A)
Published: 2018-04-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: recombination

Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A). Determined by electron microscopy at 3.17 Å resolution. Released 25 Apr 2018.

Method: Electron microscopy
Resolution: 3.17 Å
Organisms: Mus musculus, Escherichia coli K-12, Homo sapiens
Chains: 11
Atoms: 20,080
Mol. weight: 373.4 kDa
Ligands: CA, ZN
Released: 25 Apr 2018

Explore 6CG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CG0 contains 77 α-helices and 110 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: 31 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	405-418	14
α-helix	419-423	5
α-helix	427-441	15
α-helix	445-454	10
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	535-536	2	1
β-strand	554-556	3	1
α-helix	559-569	11
α-helix	571-580	10
β-strand	590-601	12	1
α-helix	606-608	3
β-strand	620-631	12	1
β-strand	638-642	5	1
α-helix	649-651	3
β-strand	653-658	6	1
α-helix	665-682	18
β-strand	687-688	2	1
β-strand	690-691	2	2
β-strand	694-695	2	2
β-strand	697-706	10	1
α-helix	709-716	8
α-helix	734-739	6
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-840	18
α-helix	852-857	6
α-helix	860-866	7
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-923	15
α-helix	925-928	4
α-helix	935-941	7
α-helix	943-950	8
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1003	7

Chain B: 6 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	21
β-strand	7-8	2	22
α-helix	12-14	3
β-strand	22-23	2	22
β-strand	28-30	3	22
β-strand	46-50	5	22
β-strand	54-59	6	22
β-strand	61-62	2	23
α-helix	69-71	3
β-strand	78-80	3	24
β-strand	90-94	5	24
β-strand	97	1	25
β-strand	103	1	25
β-strand	107-110	4	24
β-strand	112-116	5	23
β-strand	119-122	4	23
β-strand	125-127	3	24
β-strand	130-131	2	26
α-helix	133-136	4
β-strand	138	1	27
β-strand	141-146	6	26
β-strand	151-156	6	26
β-strand	159-161	3	27
α-helix	169-171	3
β-strand	175-177	3	27
β-strand	182-186	5	26
β-strand	191-195	5	26
β-strand	205	1	28
β-strand	208-211	4	29
β-strand	215-219	5	29
β-strand	222	1	28
β-strand	223	1	30
β-strand	228	1	30
β-strand	232-239	8	29
β-strand	246-256	11	29
β-strand	259	1	31
β-strand	262-267	6	32
β-strand	270-274	5	32
β-strand	277	1	31
β-strand	288-292	5	32
β-strand	297-300	4	32
α-helix	303-305	3
α-helix	309-313	5
β-strand	318-321	4	21
β-strand	326-332	7	21
β-strand	343-349	7	21

Chain C: 30 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	401-419	19
α-helix	427-441	15
α-helix	446-456	11
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-510	11
β-strand	518-519	2	3
β-strand	535-536	2	3
β-strand	554-556	3	3
α-helix	559-580	22
β-strand	590-603	14	3
α-helix	606-608	3
β-strand	618-632	15	3
β-strand	637-642	6	3
α-helix	649-651	3
β-strand	653-658	6	3
α-helix	665-682	18
β-strand	687-690	4	3
β-strand	695-706	12	3
α-helix	709-715	7
β-strand	718	1	4
β-strand	725	1	5
β-strand	733	1	5
α-helix	734-737	4
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	4
α-helix	793-811	19
α-helix	823-841	19
α-helix	843-845	3
α-helix	851-857	7
α-helix	860-867	8
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-922	14
α-helix	923-926	4
α-helix	934-941	8
α-helix	943-949	7
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-995	13
α-helix	1000-1003	4

Chain D: 6 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	6
β-strand	7	1	7
α-helix	12-14	3
β-strand	22-24	3	8
β-strand	27-30	4	8
β-strand	46-48	3	8
β-strand	50	1	9
β-strand	54	1	7
β-strand	55	1	9
β-strand	58	1	8
β-strand	61-62	2	10
α-helix	69-71	3
β-strand	75	1	11
β-strand	78-81	4	12
β-strand	89-93	5	12
β-strand	95	1	11
β-strand	97	1	13
β-strand	103	1	13
β-strand	107-111	5	12
β-strand	112-116	5	10
β-strand	119-122	4	10
β-strand	125-127	3	12
β-strand	130-131	2	14
α-helix	133-136	4
β-strand	138	1	15
β-strand	142-146	5	14
β-strand	151-155	5	14
β-strand	159-161	3	15
α-helix	169-171	3
β-strand	175-177	3	15
α-helix	178-179	2
β-strand	182-185	4	14
β-strand	191-195	5	14
β-strand	205	1	16
β-strand	208-211	4	17
β-strand	215-219	5	17
β-strand	222	1	16
β-strand	223	1	18
β-strand	228	1	18
β-strand	233-239	7	17
β-strand	246-252	7	17
β-strand	259	1	19
β-strand	263-267	5	20
β-strand	270-273	4	20
β-strand	277	1	19
β-strand	283	1	19
β-strand	288-291	4	20
β-strand	299-301	3	20
α-helix	303-305	3
β-strand	318-321	4	6
β-strand	326-332	7	6
β-strand	343-349	7	6

Chain N: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	18-26	9
α-helix	42-47	6
α-helix	101-116	16
α-helix	122-135	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A, C	protein	775	Mus musculus	P15919 (AlphaFold model)
V(D)J recombination-activating protein 2	B, D	protein	520	Mus musculus	P21784 (AlphaFold model)
DNA (46-mer)	F	DNA	46	Escherichia coli K-12
DNA (5'-d(gpaptpcptpgpgpcpcptpgptpcptptpa)-3')	I	DNA	16	Homo sapiens
DNA (5'-d(pcptpgpgpaptpcptpgpgpcpcptpgptpcptptp*a)-3')	J	DNA	19	Escherichia coli K-12
DNA (60-mer)	G	DNA	60	Escherichia coli K-12
DNA (30-mer)	L	DNA	30	Escherichia coli K-12
DNA (41-mer)	M	DNA	41	Escherichia coli K-12
High mobility group protein B1	N	protein	126	Homo sapiens	P09429 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6CG0_1 V(D)J recombination-activating protein 1 (chains A, C)
NCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY
CPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKESKETLV
HINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNE
HRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALR
NAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALV
SALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSF
TVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKS
SELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFH
SITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEF
YKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVD
AVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKF
KYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEM
EDVLKHHWLYTSKYLQKFMNAHNALKSSGFTMNSKETLGDPLGIEDSLESQDSME

Sequence of entity 2 (B, D), FASTA

>6CG0_2 V(D)J recombination-activating protein 2 (chains B, D)
MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPA
IFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKV
TFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLP
HVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDL
PLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEIS
EMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQK
IVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCC
PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNE
HVQIARALQAPKRNPPLQKPPMKSLHKKGSGKVLTPAKKS

Sequence of entity 3 (F), FASTA

>6CG0_3 DNA (46-MER) (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGATC

Sequence of entity 4 (I), FASTA

>6CG0_4 DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') (chains I)
GATCTGGCCTGTCTTA

Sequence of entity 5 (J), FASTA

>6CG0_5 DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') (chains J)
CTGGATCTGGCCTGTCTTA

Sequence of entity 6 (G), FASTA

>6CG0_6 DNA (60-MER) (chains G)
CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGATCCAG

Sequence of entity 7 (L), FASTA

>6CG0_7 DNA (30-MER) (chains L)
CACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 8 (M), FASTA

>6CG0_8 DNA (41-MER) (chains M)
CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCCG

Sequence of entity 9 (N), FASTA

>6CG0_9 High mobility group protein B1 (chains N)
SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYERE
MKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN
NTAADD

Ligands and cofactors

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

Primary citation

Cracking the DNA Code for V(D)J Recombination. Kim, M.S., Chuenchor, W., Chen, X. et al. Mol Cell (2018) 70:358-370.e4. DOI 10.1016/j.molcel.2018.03.008 · 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 6CG0 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.