8ODZ: Interleukin-12 subunit alpha

Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 1). Determined by electron microscopy at 3.6 Å resolution. Released 7 Feb 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Mus musculus
Chains: 4
Atoms: 12,100
Mol. weight: 213.13 kDa
Ligands: NAG
Released: 7 Feb 2024

Explore 8ODZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ODZ contains 21 α-helices and 122 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	33-54	22
α-helix	77-80	4
α-helix	84-86	3
α-helix	109-111	3
α-helix	116-140	25
α-helix	153-166	14
α-helix	186-213	28

Chain B: 2 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	30-32	3	1
β-strand	35-36	2	2
β-strand	44-49	6	3
β-strand	59-62	4	1
β-strand	70-71	2	1
β-strand	74-79	6	3
β-strand	86-92	7	1
β-strand	95-102	8	1
β-strand	104	1	4
β-strand	106-108	3	2
β-strand	111-112	2	2
β-strand	117-118	2	5
β-strand	127-129	3	5
β-strand	136-143	8	5
β-strand	149-150	2	4
β-strand	153-154	2	4
β-strand	165	1	6
β-strand	170-179	10	5
β-strand	182-192	11	5
β-strand	193	1	6
α-helix	205	1
β-strand	206-214	9	4
β-strand	217-225	9	4
β-strand	240-244	5	7
β-strand	248-252	5	7
β-strand	268-269	2	8
β-strand	270-274	5	9
β-strand	294-296	3	9
β-strand	300-303	4	7
β-strand	310-312	3	9
β-strand	315-316	2	8
α-helix	321-323	3
β-strand	327-329	3	9

Chain C: 5 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	47-56	10	10
β-strand	60-68	9	10
β-strand	75-82	8	11
β-strand	94-99	6	11
β-strand	120-128	9	11
β-strand	131-134	4	11
β-strand	138-140	3	11
β-strand	146-147	2	10
α-helix	148-150	3
α-helix	154-155	2
β-strand	156-160	5	12
β-strand	163-169	7	12
β-strand	177-183	7	13
β-strand	189-193	5	13
β-strand	213-218	6	12
β-strand	225-232	8	13
β-strand	234	1	14
β-strand	240	1	14
α-helix	243-247	5
β-strand	251-253	3	13
β-strand	276-279	4	15
β-strand	303-310	8	16
β-strand	320-324	5	16
β-strand	328-331	4	15
β-strand	336-343	8	16
β-strand	348	1	16
β-strand	352-356	5	16
β-strand	368-372	5	17
β-strand	375-379	5	17
β-strand	389-395	7	18
β-strand	404-407	4	18
β-strand	420-423	4	17
β-strand	434-441	8	18
β-strand	452-460	9	18
α-helix	464-467	4
β-strand	471-477	7	19
β-strand	483-488	6	19
β-strand	499-508	10	20
β-strand	514-519	6	20
β-strand	525-528	4	19
α-helix	531-532	2
β-strand	537-545	9	20
β-strand	556-558	3	20

Chain D: 7 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	31-36	6	21
β-strand	40-41	2	22
β-strand	47-53	7	21
β-strand	69-74	6	22
β-strand	77-80	4	22
α-helix	91-93	3
β-strand	94-99	6	21
β-strand	106-112	7	22
β-strand	125-133	9	22
α-helix	136-140	5
β-strand	141-148	8	23
β-strand	154-159	6	23
β-strand	168-176	9	24
β-strand	180-188	9	24
β-strand	196-198	3	23
β-strand	211-219	9	24
β-strand	225	1	24
β-strand	230-233	4	24
α-helix	234-236	3
β-strand	238-239	2	23
α-helix	240-242	3
β-strand	244-250	7	25
β-strand	258-263	6	25
β-strand	270-277	8	26
β-strand	284-289	6	26
β-strand	294-297	4	25
β-strand	306-313	8	26
β-strand	328-330	3	26
β-strand	344	1	27
β-strand	347-348	2	27
β-strand	355-360	6	27
β-strand	375	1	28
β-strand	376-382	7	29
β-strand	387-393	7	29
β-strand	397-402	6	27
β-strand	408-412	5	29
β-strand	415	1	28
β-strand	420	1	28
β-strand	424-428	5	29
β-strand	443-448	6	30
β-strand	451-455	5	30
β-strand	468-475	8	31
α-helix	485-486	2
β-strand	487-491	5	31
β-strand	497-500	4	30
β-strand	508	1	32
β-strand	510-517	8	31
β-strand	523-529	7	31
β-strand	544-548	5	33
β-strand	551-555	5	33
α-helix	561-564	4
β-strand	566	1	32
β-strand	570-577	8	34
α-helix	583-584	2
β-strand	585-590	6	34
β-strand	597-600	4	33
β-strand	609-616	8	34
β-strand	621	1	34
β-strand	628-630	3	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 subunit alpha	A	protein	231	Mus musculus	P43431 (AlphaFold model)
Interleukin-12 subunit beta	B	protein	313	Mus musculus	P43432 (AlphaFold model)
Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1	C	protein	572	Mus musculus	P53355 (AlphaFold model)
Interleukin-12 receptor subunit beta-2,Calmodulin-1	D	protein	769	Mus musculus	P0DP26 (AlphaFold model), P97378

Sequence of entity 1 (A), FASTA

>8ODZ_1 Interleukin-12 subunit alpha (chains A)
RVIPVSGPARCLSQSRNLLKTTDDMVKTAREKLKHYSCTAEDIDHEDITRDQTSTLKTCL
PLELHKNESCLATRETSSTTRGSCLPPQKTSLMMTLCLGSIYEDLKMYQTEFQAINAALQ
NHNHQQIILDKGMLVAIDELMQSLNHNGETLRQKPPVGEADPYRVKMKLCILLHAFSTRV
VTINRVMGYLSSAGTSDEVDGGSGGSGLNDIFEAQKIEWHEGRTKHHHHHH

Sequence of entity 2 (B), FASTA

>8ODZ_2 Interleukin-12 subunit beta (chains B)
MWELEKDVYVVEVDWTPDAPGETVNLTCDTPEEDDITWTSDQRHGVIGSGKTLTITVKEF
LDAGQYTCHKGGETLSHSHLLLHKKENGIWSTEILKNFKNKTFLKCEAPNYSGRFTCSWL
VQRNMDLKFNIKSSSSSPDSRAVTCGMASLSAEKVTLDQRDYEKYSVSCQEDVTCPTAEE
TLPIELALEARQQNKYENYSTSFFIRDIIKPDPPKNLQMKPLKNSQVEVSWEYPDSWSTP
HSYFSLKFFVRIQRKKEKMKETEEGCNQKGAFLVEKTSTEVQCKGGNVCVQAQDRYYNSS
CSKWACVPCRVRS

Sequence of entity 3 (C), FASTA

>8ODZ_3 Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 (chains C)
QLGASGPGDGCCVEKTSFPEGASGSPLGPRNLSCYRVSKTDYECSWQYDGPEDNVSHVLW
CCFVPPNHTHTGQERCRYFSSGPDRTVQFWEQDGIPVLSKVNFWVESRLGNRTMKSQKIS
QYLYNWTKTTPPLGHIKVSQSHRQLRMDWNVSEEAGAEVQFRRRMPTTNWTLGDCGPQVN
SGSGVLGDIRGSMSESCLCPSENMAQEIQIRRRRRLSSGAPGGPWSDWSMPVCVPPEVLP
QAKIKFLVEPLNQGGRRRLTMQGQSPQLAVPEGCRGRPGAQVKKHLVLVRMLSCRCQAQT
SKTVPLGKKLNLSGATYDLNVLAKTRFGRSTIQKWHLPAQELTETRALNVSVGGNMTSMQ
WAAQAPGTTYCLEWQPWFQHRNHTHCTLIVPEEEDPAKMVTHSWSSKPTLEQEECYRITV
FASKNPKNPMLWATVLSSYYFGGNASRAGTPRHVSVRNQTGDSVSVEWTASQLSTCPGVL
TQYVVRCEAEDGAWESEWLVPPTKTQVTLDGLRSRVMYKVQVRADTARLPGAWSHPQRFS
FEGTGGSGGSGGAARKKWKQSVRLISLCQRLS

Sequence of entity 4 (D), FASTA

>8ODZ_4 Interleukin-12 receptor subunit beta-2,Calmodulin-1 (chains D)
NIDVCKLGTVTVQPAPVIPLGSAANISCSLNPKQGCSHYPSSNELILLKFVNDVLVENLH
GKKVHDHTGHSSTFQVTNLSLGMTLFVCKLNCSNSQKKPPVPVCGVEISVGVAPEPPQNI
SCVQEGENGTVACSWNSGKVTYLKTNYTLQLSGPNNLTCQKQCFSDNRQNCNRLDLGINL
SPDLAESRFIVRVTAINDLGNSSSLPHTFTFLDIVIPLPPWDIRINFLNASGSRGTLQWE
DEGQVVLNQLRYQPLNSTSWNMVNATNAKGKYDLRDLRPFTEYEFQISSKLHLSGGSWSN
WSESLRTRTPEEEPVGILDIWYMKQDIDYDRQQISLFWKSLNPSEARGKILHYQVTLQEV
TKKTTLQNTTRHTSWTRVIPRTGAWTASVSAANSKGASAPTHINIVDLCGTGLLAPHQVS
AKSENMDNILVTWQPPKKADSAVREYIVEWRALQPGSITKFPPHWLRIPPDNMSALISEN
IKPYICYEIRVHALSESQGGCSSIRGDSKHKAPVSGPHITAITEKKERLFISWTHIPFPE
QRGCILHYRIYWKERDSTAQPELCEIQYRRSQNSHPISSLQPRVTYVLWMTAVTAAGESP
QGNEREFCPQGKANGTGGSGGSGGLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSL
GQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGY
ISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23. Bloch, Y., Felix, J., Merceron, R. et al. Nat Struct Mol Biol (2024) 31:591-597. DOI 10.1038/s41594-023-01190-6 · PubMed

Other PDB entries of the same protein (UniProt P43431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CR6 2.85 Å, mouse Interleukin-12
8PB1 3.5 Å, Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling…
8OE0 4.6 Å, Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling…

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