8ODX: Interleukin-12 receptor subunit beta-1

Interleukin 12 receptor subunit beta-1 Fn domains in complex with antagonistic FAb4 fragment and VHH. Determined by X-ray diffraction at 4.4 Å resolution. Released 7 Feb 2024.

Method: X-ray diffraction
Resolution: 4.4 Å
Organisms: Homo sapiens, Homo sapiens x Mus musculus hybrid cell line, Lama glama
Chains: 4
Atoms: 6,382
Mol. weight: 110.92 kDa
Released: 7 Feb 2024

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

Secondary structure: helices and β-sheets

8ODX contains 27 α-helices and 79 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: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	241-245	5	1
α-helix	246-248	3
β-strand	254-255	2	2
β-strand	256-260	5	1
β-strand	281-288	8	3
β-strand	298-302	5	3
β-strand	308-309	2	2
β-strand	314-321	8	3
β-strand	329-334	6	3
β-strand	340	1	4
α-helix	344-345	2
β-strand	348-350	3	5
β-strand	353-359	7	5
β-strand	365	1	6
β-strand	366-373	8	4
β-strand	382-385	4	4
α-helix	386-388	3
β-strand	389	1	6
α-helix	390-392	3
β-strand	396-402	7	5
β-strand	413-421	9	4
α-helix	427-429	3
β-strand	431-439	9	4
α-helix	443-446	4
β-strand	453-458	6	7
β-strand	461-465	5	7
α-helix	467-469	3
α-helix	470-473	4
β-strand	480-487	8	8
β-strand	493-498	6	8
β-strand	504-508	5	7
β-strand	515-523	9	8
α-helix	528-534	7
β-strand	535-538	4	8

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	110-111	2	10
β-strand	115-119	5	10
β-strand	125	1	11
α-helix	126-127	2
β-strand	128-132	5	12
α-helix	133-135	3
β-strand	143-153	11	12
β-strand	154	1	11
β-strand	159-162	4	13
β-strand	171-173	3	12
α-helix	174-176	3
β-strand	177-178	2	12
β-strand	184-193	10	12
α-helix	194-196	3
β-strand	202-208	7	13
α-helix	209-211	3
β-strand	213-219	7	13

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	18-25	8	14
β-strand	34-39	6	15
β-strand	46-51	6	15
β-strand	58-60	3	15
β-strand	68-73	6	14
α-helix	74-76	3
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-99	8	15
β-strand	108-111	4	15
β-strand	115-119	5	15

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
β-strand	9-12	4	17
β-strand	18-24	7	16
β-strand	32-37	6	17
β-strand	44-48	5	17
β-strand	52-53	2	17
α-helix	54	1
β-strand	61-66	6	16
β-strand	69-74	6	16
α-helix	79-81	3
β-strand	84-89	6	17
α-helix	95	1
β-strand	96-97	2	17
β-strand	98	1	16
β-strand	101-105	5	17
β-strand	110	1	18
β-strand	113-117	5	19
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	19
β-strand	139	1	18
β-strand	143-149	7	20
β-strand	152-153	2	20
α-helix	154	1
β-strand	158-162	5	19
α-helix	163-166	4
β-strand	172-181	10	19
α-helix	182-186	5
β-strand	190-197	8	20
β-strand	204-209	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 receptor subunit beta-1	A	protein	376	Homo sapiens	P42701 (AlphaFold model)
FAb4 Heavy chain	H	protein	250	Homo sapiens x Mus musculus hybrid cell line
anti Kappa Light chain VHH	K	protein	167	Lama glama
FAb4 Light chain	L	protein	231	Homo sapiens x Mus musculus hybrid cell line

Sequence of entity 1 (A), FASTA

>8ODX_1 Interleukin-12 receptor subunit beta-1 (chains A)
MGILPSPGMPALLSLVSLLSVLLMGCVAEPPENPPQPQVRFSVEQLGQDGRRRLTLKEQP
TQLELPEGCQGLAPGTEVTYRLQLHMLSCPCKAKATRTLHLGKMPYLSGAAYNVAVISSN
QFGPGLNQTWHIPADTHTEPVALNISVGTNGTTMYWPARAQSMTYCIEWQPVGQDGGLAT
CSLTAPQDPDPAGMATYSWSRESGAMGQEKCYYITIFASAHPEKLTLWSTVLSTYHFGGN
ASAAGTPHHVSVKNHSLDSVSVDWAPSLLSTCPGVLKEYVVRCRDEDSKQVSEHPVQPTE
TQVTLSGLRAGVAYTVQVRADTAWLRGVWSQPQRFSIEGTSDEVDGGSGGSGLNDIFEAQ
KIEWHEGRTKHHHHHH

Sequence of entity 2 (H), FASTA

>8ODX_2 FAb4 Heavy chain (chains H)
MGWSCIILFLVATATGVHSQVQLVESGGGVVQPGRSLRLSCAASGFTFTSYGMSWVRQAP
GKGLEWVAGISYDASDTEYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARSPD
YIIDYGFDYWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS
WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP
KSCGHHHHHH

Sequence of entity 3 (K), FASTA

>8ODX_3 anti Kappa Light chain VHH (chains K)
MGKYLLPTAAAGLLLLAAQPAMAHHHHHHSSGLVPRGSHMSDEVDGQVQLQESGGGLVQP
GGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDD
AKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Sequence of entity 4 (L), FASTA

>8ODX_4 FAb4 Light chain (chains L)
MGVKVLFALICIAVAEAAIQMTQSPSSLSASVGDRVTITCRASQGISSDLAWYQQKPGKA
PKLLIYDASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYWWYPFTFGQGTK
VEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESV
TEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 P42701 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WDP 2.01 Å, Interleukin 12 receptor subunit beta-1
8C7M 2.56 Å, Interleukin 12 receptor subunit beta-1 Fn domains in complex with antagonistic FAb…
6WDQ 3.4 Å, IL23/IL23R/IL12Rb1 signaling complex
8YI7 3.57 Å, The Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2…
8OE4 3.6 Å, Cryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex.
8XRP 3.75 Å, The Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2…

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