4WWX: Core RAG1/2 recombinase

Crystal structure of the core RAG1/2 recombinase. Determined by X-ray diffraction at 3.2 Å resolution. Released 25 Feb 2015.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 14,978
Mol. weight: 219.72 kDa
Ligands: ZN
Released: 25 Feb 2015

Explore 4WWX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WWX contains 70 α-helices and 92 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 B: 30 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	396-398	3
α-helix	401-421	21
α-helix	427-441	15
α-helix	445-455	11
α-helix	464-473	10
α-helix	478-492	15
α-helix	500-510	11
β-strand	517-520	4	1
α-helix	522-523	2
β-strand	534-536	3	1
β-strand	554-557	4	1
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-604	14	1
β-strand	618-633	16	1
β-strand	636-642	7	1
β-strand	653-658	6	1
α-helix	665-683	19
β-strand	686-690	5	1
β-strand	695-707	13	1
α-helix	709-716	8
α-helix	736-739	4
α-helix	750-762	13
α-helix	769-776	8
α-helix	793-812	20
α-helix	823-840	18
α-helix	851-857	7
α-helix	860-866	7
α-helix	867-869	3
α-helix	874-894	21
α-helix	898-901	4
α-helix	903-907	5
α-helix	909-921	13
α-helix	934-950	17
α-helix	954-956	3
α-helix	964-973	10
α-helix	980-994	15
α-helix	997-1003	7
α-helix	1005-1007	3

Chain E: 29 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	407-422	16
α-helix	427-440	14
α-helix	445-455	11
α-helix	464-473	10
α-helix	478-492	15
α-helix	498-499	2
α-helix	500-509	10
β-strand	518-519	2	12
α-helix	522-523	2
β-strand	534-536	3	12
β-strand	554-557	4	12
α-helix	559-569	11
α-helix	571-580	10
β-strand	591-604	14	12
β-strand	618-633	16	12
β-strand	636-642	7	12
β-strand	653-658	6	12
α-helix	665-683	19
β-strand	687-690	4	12
β-strand	695-707	13	12
α-helix	709-716	8
β-strand	718	1	13
α-helix	736-739	4
α-helix	750-762	13
α-helix	769-776	8
β-strand	779	1	13
α-helix	793-812	20
α-helix	823-841	19
α-helix	851-857	7
α-helix	860-866	7
α-helix	867-869	3
α-helix	874-894	21
α-helix	903-907	5
α-helix	909-921	13
α-helix	934-950	17
α-helix	954-956	3
α-helix	964-973	10
α-helix	980-994	15
α-helix	997-1003	7
α-helix	1005-1007	3

Chain X: 6 helices, 36 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
α-helix	37-38	2
β-strand	45-51	7	3
β-strand	54-59	6	3
β-strand	61-62	2	4
β-strand	76-80	5	4
β-strand	90-94	5	4
β-strand	96-97	2	5
β-strand	103-104	2	5
β-strand	107-115	9	4
β-strand	120-127	8	4
β-strand	130	1	6
α-helix	133-135	3
β-strand	138	1	7
β-strand	141-145	5	6
β-strand	152-156	5	6
β-strand	159-161	3	7
α-helix	162-163	2
α-helix	169-171	3
β-strand	175-177	3	7
β-strand	182-186	5	6
β-strand	191-195	5	6
β-strand	208-212	5	8
β-strand	215-219	5	8
β-strand	233-237	5	8
β-strand	249-252	4	8
β-strand	259	1	9
β-strand	262-267	6	10
β-strand	270-274	5	10
β-strand	277	1	9
β-strand	279	1	11
β-strand	282	1	11
β-strand	288-291	4	10
β-strand	298-300	3	10
α-helix	309-312	4
β-strand	318-321	4	2
β-strand	327-331	5	2
β-strand	344-348	5	2

Chain Y: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	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	61-62	2	16
β-strand	76-80	5	16
β-strand	90-94	5	16
β-strand	96-97	2	17
β-strand	103-104	2	17
β-strand	107-112	6	16
β-strand	121-127	7	16
β-strand	130	1	18
α-helix	133-135	3
β-strand	138	1	19
β-strand	141-145	5	18
β-strand	152-156	5	18
β-strand	159-160	2	19
α-helix	161-163	3
β-strand	176-177	2	19
α-helix	181	1
β-strand	182-186	5	18
β-strand	191-195	5	18
β-strand	208-212	5	20
β-strand	215-219	5	20
β-strand	233-238	6	20
β-strand	247-252	6	20
β-strand	259	1	21
β-strand	263-267	5	22
β-strand	270-273	4	22
β-strand	277	1	21
β-strand	279	1	23
β-strand	282	1	23
β-strand	289-291	3	22
β-strand	298-300	3	22
α-helix	309-312	4
β-strand	318-321	4	14
β-strand	327-331	5	14
β-strand	344-348	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	B, E	protein	618	Mus musculus	P15919 (AlphaFold model)
V(D)J recombination-activating protein 2	X, Y	protein	349	Mus musculus	P21784 (AlphaFold model)

Sequence of entity 1 (B, E), FASTA

>4WWX_1 V(D)J recombination-activating protein 1 (chains B, E)
APRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADE
LEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVL
LPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDM
EEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRIT
IEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLE
MGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSH
AENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQL
EIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELI
PSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEG
KITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKH
HWLYTSKYLQKFMNAHNA

Sequence of entity 2 (X, Y), FASTA

>4WWX_2 V(D)J recombination-activating protein 2 (chains X, Y)
SLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAI
FSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVT
FRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPH
VFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLP
LGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISE
METPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Crystal structure of the V(D)J recombinase RAG1-RAG2. Kim, M.S., Lapkouski, M., Yang, W. et al. Nature (2015) 518:507-511. DOI 10.1038/nature14174 · 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

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