8OE4: Interleukin-12 subunit beta

Cryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex. Determined by electron microscopy at 3.6 Å resolution. Released 7 Feb 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,951
Mol. weight: 172.19 kDa
Ligands: NAG
Released: 7 Feb 2024

Explore 8OE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OE4 contains 37 α-helices and 97 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: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	30-36	7	1
β-strand	44-49	6	2
β-strand	59-62	4	1
β-strand	71	1	1
β-strand	74-79	6	2
β-strand	87-92	6	1
β-strand	95-108	14	1
β-strand	111-112	2	1
β-strand	117-118	2	3
α-helix	119	1
β-strand	130-132	3	3
β-strand	133	1	4
β-strand	139-146	8	3
β-strand	152-153	2	1
β-strand	156-160	5	3
β-strand	168-170	3	3
β-strand	174-181	8	3
β-strand	184-195	12	3
α-helix	203-204	2
β-strand	208-212	5	3
β-strand	215-216	2	1
β-strand	219-220	2	1
β-strand	223-227	5	3
α-helix	229-231	3
β-strand	233	1	4
α-helix	235-238	4
β-strand	239-245	7	5
α-helix	246	1
β-strand	251-257	7	5
β-strand	271-279	9	6
β-strand	289	1	6
β-strand	295-299	5	5
β-strand	304-312	9	6
α-helix	319-322	4
β-strand	323-326	4	6

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	30-47	18
β-strand	57	1	7
α-helix	79-84	6
α-helix	86-104	19
α-helix	107-110	4
α-helix	114-116	3
α-helix	120-135	16
α-helix	157-186	30

Chain C: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	8
β-strand	41-43	3	7
β-strand	48-54	7	8
β-strand	63-68	6	7
β-strand	71	1	7
β-strand	77-78	2	8
β-strand	84-89	6	8
β-strand	96-104	9	7
β-strand	111-122	12	7
α-helix	124-128	5
β-strand	132-136	5	9
β-strand	141-145	5	9
β-strand	157-164	8	10
β-strand	170-175	6	10
β-strand	179-182	4	9
α-helix	183-185	3
β-strand	191-199	9	10
β-strand	204-206	3	10
α-helix	207-209	3
β-strand	210-213	4	10
β-strand	218-219	2	9
α-helix	221-222	2
β-strand	223-231	9	11
β-strand	237-244	8	11
β-strand	251-259	9	12
β-strand	266-272	7	12
β-strand	278-283	6	11
β-strand	289-298	10	12
α-helix	305-310	6
β-strand	311-314	4	12

Chain D: 19 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	13
β-strand	47-54	8	14
β-strand	59-66	8	14
β-strand	73-80	8	13
β-strand	86-92	7	13
β-strand	96-100	5	14
α-helix	101-103	3
β-strand	111-119	9	13
β-strand	122-124	3	13
β-strand	129-131	3	13
α-helix	139-142	4
β-strand	146-151	6	15
β-strand	154-159	6	15
β-strand	160	1	16
α-helix	161-162	2
β-strand	168-175	8	17
β-strand	182-189	8	17
β-strand	193	1	16
β-strand	196-198	3	15
β-strand	206-214	9	17
α-helix	222-226	5
α-helix	228	1
β-strand	229-231	3	17
α-helix	236-238	3
β-strand	242-245	4	18
α-helix	246-249	4
β-strand	253-255	3	19
β-strand	256-260	5	18
α-helix	261-266	6
α-helix	276-278	3
α-helix	279-280	2
β-strand	281-288	8	20
β-strand	298-302	5	20
α-helix	306-307	2
β-strand	308-310	3	19
β-strand	314-322	9	20
β-strand	325-326	2	20
β-strand	330-334	5	20
α-helix	335-337	3
β-strand	346-349	4	21
β-strand	353-359	7	21
β-strand	365-373	9	22
α-helix	379-381	3
β-strand	382-389	8	22
β-strand	396-402	7	21
β-strand	412-421	10	22
α-helix	427-429	3
β-strand	431-440	10	22
α-helix	443-446	4
β-strand	450-458	9	23
β-strand	461-467	7	23
α-helix	468-469	2
α-helix	470-473	4
β-strand	478-487	10	24
β-strand	493-498	6	24
β-strand	504-508	5	23
α-helix	510-511	2
β-strand	515-524	10	24
α-helix	528-534	7
β-strand	535-538	4	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 subunit beta	A	protein	306	Homo sapiens	P29460 (AlphaFold model)
Interleukin-23 subunit alpha	B	protein	186	Homo sapiens	Q9NPF7 (AlphaFold model)
Interleukin-23 receptor,Calmodulin-1	C	protein	485	Homo sapiens	P0DP23 (AlphaFold model), Q5VWK5 (AlphaFold model)
Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1	D	protein	547	Homo sapiens	P42701, P53355

Sequence of entity 1 (A), FASTA

>8OE4_1 Interleukin-12 subunit beta (chains A)
IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEF
GDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTC
WWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAA
EESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTW
STPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKDASISVRAQDRYYSSSWSEW
ASVPCS

Sequence of entity 2 (B), FASTA

>8OE4_2 Interleukin-23 subunit alpha (chains B)
RAVPGGSSPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEGDEETTNDVPHIQCGDGCDP
QGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSPVGQLHASLLGLSQLLQPEG
HHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVFAHGAATLSPGDEVDGHHHH
HHHHHH

Sequence of entity 3 (C), FASTA

>8OE4_3 Interleukin-23 receptor,Calmodulin-1 (chains C)
GITNINCSGHIWVEPATIFKMGMNISIYCQAAIKNCQPRKLHFYKNGIKERFQITRINKT
TARLWYKNFLEPHASMYCTAECPKHFQETLICGKDISSGYPPDIPDEVTCVIYEYSGNMT
CTWNAGKLTYIDTKYVVHVKSLETEEEQQYLTSSYINISTDSLQGGKKYLVWVQAANALG
MEESKQLQIHLDDIVIPSAAVISRAETINATVPKTIIYWDSQTTIEKVSCEMRYKATTNQ
TWNVKEFDTNFTYVQQSEFYLEPNIKYVFQVRCQETGKRYWQPWSSLFFHKTPETVPQVT
SKAFQHDTWNSGLTVASISTGHLTSDNRGDGTGGSGGSGGLTEEQIAEFKEAFSLFDKDG
DGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEE
EIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQ
MMTAK

Sequence of entity 4 (D), FASTA

>8OE4_4 Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 (chains D)
CRTSECCFQDPPYPDADSGSASGPRDLRCYRISSDRYECSWQYEGPTAGVSHFLRCCLSS
GRCCYFAAGSATRLQFSDQAGVSVLYTVTLWVESWARNQTEKSPEVTLQLYNSVKYEPPL
GDIKVSKLAGQLRMEWETPDNQVGAEVQFRHRTPSSPWKLGDCGPQDDDTESCLCPLEMN
VAQEFQLRRRQLGSQGSSWSKWSSPVCVPPENPPQPQVRFSVEQLGQDGRRRLTLKEQPT
QLELPEGCQGLAPGTEVTYRLQLHMLSCPCKAKATRTLHLGKMPYLSGAAYNVAVISSNQ
FGPGLNQTWHIPADTHTEPVALNISVGTNGTTMYWPARAQSMTYCIEWQPVGQDGGLATC
SLTAPQDPDPAGMATYSWSRESGAMGQEKCYYITIFASAHPEKLTLWSTVLSTYHFGGNA
SAAGTPHHVSVKNHSLDSVSVDWAPSLLSTCPGVLKEYVVRCRDEDSKQVSEHPVQPTET
QVTLSGLRAGVAYTVQVRADTAWLRGVWSQPQRFSIEGTGGSGGSGGAARKKWKQSVRLI
SLCQRLS

Ligands and cofactors

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

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 P29460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MJ3 1.74 Å, Interleukin-23 complex with an antagonistic alphabody, crystal form 1
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
8CR8 2.0 Å, human Interleukin-23
3DUH 2.3 Å, Structure of Interleukin-23
8UUI 2.43 Å, X-ray structure of Interleukin-23 in complex with peptide 23-446
1F42 2.5 Å, The P40 domain of human interleukin-12
5MXA 2.5 Å, Structure of unbound Interleukin-23
4GRW 2.55 Å, Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs)
6UIB 2.74 Å, Crystal structure of IL23 bound to peptide 23-652
1F45 2.8 Å, Human interleukin-12
5MZV 2.8 Å, IL-23:IL-23R:Nb22E11 complex
3D87 2.9 Å, Crystal structure of Interleukin-23

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