5ZDZ: Mouse RAG1

Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Apr 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Mus musculus, synthetic construct
Chains: 11
Atoms: 20,360
Mol. weight: 311.08 kDa
Ligands: ZN, CA
Released: 25 Apr 2018

Explore 5ZDZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZDZ contains 100 α-helices and 99 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: 35 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	392-395	4
α-helix	396-398	3
α-helix	401-422	22
α-helix	427-441	15
α-helix	445-456	12
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-510	11
β-strand	517-520	4	1
α-helix	522-523	2
β-strand	534-536	3	1
β-strand	553-557	5	1
α-helix	559-569	11
α-helix	571-579	9
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	653-659	7	1
α-helix	665-682	18
β-strand	686-691	6	1
β-strand	694-706	13	1
α-helix	709-715	7
α-helix	718-720	3
α-helix	734-739	6
α-helix	750-762	13
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	860-867	8
α-helix	873-894	22
α-helix	898-901	4
α-helix	903-922	20
α-helix	925-928	4
α-helix	934-941	8
α-helix	943-950	8
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1001	5
α-helix	1002-1004	3

Chain B: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	2
β-strand	7-8	2	3
α-helix	12-14	3
β-strand	20-24	5	3
β-strand	27-31	5	3
β-strand	45-51	7	3
β-strand	54-59	6	3
β-strand	61-62	2	4
α-helix	69-71	3
β-strand	73	1	5
β-strand	76-80	5	4
β-strand	90-94	5	4
β-strand	97	1	5
α-helix	102	1
β-strand	103	1	5
α-helix	104	1
β-strand	107-114	8	4
α-helix	116-118	3
β-strand	121-126	6	4
β-strand	130-131	2	6
α-helix	133-135	3
β-strand	138	1	7
β-strand	141-147	7	6
β-strand	150-156	7	6
β-strand	159-161	3	7
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	7
α-helix	178-179	2
β-strand	182-186	5	6
β-strand	191-195	5	6
β-strand	205-212	8	8
β-strand	215-222	8	8
β-strand	223	1	9
β-strand	228	1	9
β-strand	233-239	7	8
β-strand	246-251	6	8
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	287-292	6	11
β-strand	297-302	6	11
α-helix	303-305	3
α-helix	309-313	5
β-strand	318-321	4	2
β-strand	326-332	7	2
β-strand	343-349	7	2

Chain C: 36 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	391-395	5
α-helix	396-398	3
α-helix	401-423	23
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	500-510	11
β-strand	517-520	4	12
α-helix	522-523	2
β-strand	535-536	2	12
α-helix	548-550	3
β-strand	553-556	4	12
α-helix	559-569	11
α-helix	571-580	10
α-helix	590	1
β-strand	591-603	13	12
α-helix	606-609	4
β-strand	618-632	15	12
β-strand	637-642	6	12
α-helix	649-651	3
β-strand	653-659	7	12
α-helix	665-683	19
β-strand	686-691	6	12
β-strand	694-706	13	12
α-helix	709-715	7
β-strand	725	1	13
β-strand	733	1	13
α-helix	734-737	4
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-813	21
α-helix	815-817	3
α-helix	823-841	19
α-helix	851-857	7
α-helix	860-867	8
α-helix	873-894	22
α-helix	898-901	4
α-helix	903-921	19
α-helix	925-928	4
α-helix	934-941	8
α-helix	943-950	8
α-helix	954-956	3
α-helix	959-974	16
α-helix	983-994	12
α-helix	997-1003	7

Chain D: 11 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	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	45-51	7	15
β-strand	54-59	6	15
β-strand	61-62	2	16
α-helix	69-71	3
β-strand	73	1	17
β-strand	76-80	5	16
β-strand	90-94	5	16
β-strand	97	1	17
α-helix	102	1
β-strand	103	1	17
α-helix	104	1
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	162-163	2
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	205	1	20
β-strand	208-212	5	21
β-strand	215-219	5	21
β-strand	222	1	20
β-strand	223	1	22
β-strand	228	1	22
β-strand	233-239	7	21
β-strand	246-252	7	21
β-strand	259	1	23
β-strand	262-266	5	24
β-strand	270-274	5	24
β-strand	277	1	23
β-strand	287-292	6	24
β-strand	297-302	6	24
α-helix	303-305	3
α-helix	309-313	5
β-strand	318-321	4	14
β-strand	326	1	25
β-strand	327-332	6	14
β-strand	343-346	4	14
β-strand	349	1	25

Chain N: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	15-30	16
α-helix	38-49	12
α-helix	56-75	20
α-helix	98-100	3
α-helix	101-115	15
α-helix	123-135	13
α-helix	142-156	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mouse RAG1	A, C	protein	627	Mus musculus	P15919 (AlphaFold model)
mouse RAG2	B, D	protein	389	Mus musculus	P21784 (AlphaFold model)
HMGB1 A-B box	N	protein	163	Mus musculus	P63158 (AlphaFold model)
DNA (5'-d(tpaptpcptpgpgpcpcptpgptpcptptpa)-3')	F	DNA	45	synthetic construct
DNA (54-mer)	I	DNA	16	synthetic construct
DNA (30-mer)	J	DNA	16	synthetic construct
DNA (39-mer)	G	DNA	54	synthetic construct
DNA chain L	L	DNA	30	synthetic construct
DNA chain M	M	DNA	39	synthetic construct

Sequence of entity 1 (A, C), FASTA

>5ZDZ_1 mouse RAG1 (chains A, C)
GPVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRA
RNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLH
ALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDS
ALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVR
FSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREA
MKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNL
VFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNA
AEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQE
TVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLS
TKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKC
YEMEDVLKHHWLYTSKYLQKFMNAHNA

Sequence of entity 2 (B, D), FASTA

>5ZDZ_2 mouse RAG2 (chains B, D)
GPVSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLK
PAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNK
KVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADC
LPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRV
DLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIE
ISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSED
QKIVSNSQTSTEDPGDSTPFEDSEEFCFS

Sequence of entity 3 (N), FASTA

>5ZDZ_3 HMGB1 A-B box (chains N)
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
EDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL
SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

Sequence of entity 4 (F), FASTA

>5ZDZ_4 DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') (chains F)
CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGAT

Sequence of entity 5 (I), FASTA

>5ZDZ_5 DNA (54-MER) (chains I)
AATCTGGCCTGTCTTA

Sequence of entity 6 (J), FASTA

>5ZDZ_6 DNA (30-MER) (chains J)
TATCTGGCCTGTCTTA

Sequence of entity 7 (G), FASTA

>5ZDZ_7 DNA (39-MER) (chains G)
GGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGAT

Sequence of entity 8 (L), FASTA

>5ZDZ_8 DNA chain L (chains L)
CACAGTGATACAGCCCTTAACAAAAACCCG

Sequence of entity 9 (M), FASTA

>5ZDZ_9 DNA chain M (chains M)
CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACC

Ligands and cofactors

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

Water and common crystallization additives (K, EDO) are not listed.

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+
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)
9LQV 3.1 Å, Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)

Browse structure collections

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